Advertise with Googlier.com http://answers.goldenhelix.com/questions/Question and answer forum supporting Golden Helix GenomeBrowseenCopyright Goldenhelix, 2012-2015.Thu, 23 May 2024 12:24:08 +0000http://answers.goldenhelix.com/question/526/error-code-1-for-vcf-import/Hi, can anyone help me with this error 1 code I receive when I import my VCF data into Genome Browse? I've tried both the long-hand folder search and the quicker drag and drop. It shows it in the Plot View but says: "Failed to open for writing: C:/Users.........snp-indel.genome/vcf.gz (error code 1)" Prior to importing. I unzipped this compressed file using winzip and put it in a separate folder, so not sure why it's showing the .gz suffix on the end of the file name. It's just a .vcf file i asked GB to import. I checked the Win11 folder properties and full read/write access is allowed (saw an earlier BAM import post on the community that suggested this) Any help would be appreciated as the GB software looks very useful! If it helps, I'm using version 3.1.0 and I've downloaded the full reference genome for GRCh38 too Thanks, John John HThu, 23 May 2024 12:24:08 +0000http://answers.goldenhelix.com/question/526/http://answers.goldenhelix.com/question/524/vcf-file-import/ How do I import VCF file ? Jan PriborskyWed, 20 Dec 2023 12:53:08 +0000http://answers.goldenhelix.com/question/524/http://answers.goldenhelix.com/question/522/how-can-i-tell-how-many-x-chromosomes-i-have/ Hi, I uploaded my raw dna data to the software and I'm wondering how to see how many x chromosomes I haveLexi BowenFri, 03 Nov 2023 04:02:09 +0000http://answers.goldenhelix.com/question/522/http://answers.goldenhelix.com/question/519/failed-to-login/ What happened with the server host? Neither of my collegues and I can login or reload any plot since a few hours agoJiwen SunTue, 12 Sep 2023 06:24:59 +0000http://answers.goldenhelix.com/question/519/http://answers.goldenhelix.com/question/494/how-can-i-fix-toolbars-controls-option-change/I would like to modify the application of the "Filter Duplicate Alignments" default option in the toolbar control. Can I make it automatically applied when I open the data? Thanks!!Kyeongsu HaWed, 21 Dec 2022 18:37:22 +0000http://answers.goldenhelix.com/question/494/http://answers.goldenhelix.com/question/495/how-to-use-bam-file-with-a-reference-to-visualize-a-gene-and-its-location/ Hi there, I am new user of genome browse. I want to see the alignment and location of some genes whose counts are differed during gene count from two different mapping methods. I want to visualize those genes and their proximities. For that, I picked a ref. genome and a relevant .bam file (by File > plot > browse, the location and the bam file) on the genome browse page but it shows "Data for this zoom level is unavailable until background computation is complete. Try zomming in". What does it mean? I looked in the manual but could not infer the solution of my problem. Please suggest me how to properly visulaize a mapped (.bam) file with a reference geneome. Thank you. VibhaVibha TripathiMon, 30 Jan 2023 12:28:55 +0000http://answers.goldenhelix.com/question/495/http://answers.goldenhelix.com/question/492/can-genomebrowse-create-sashimi-like-plots-of-exon-usage-of-rna-seq-bams/I was wondering if GenomeBrowse is capable of creating Sashimi like plots for exon usage/read counts from RNA-seq BAM files? Cheers! N OwenMon, 07 Nov 2022 11:54:20 +0000http://answers.goldenhelix.com/question/492/http://answers.goldenhelix.com/question/479/how-can-i-load-a-file-in-cram-format-into-my-gh-browser/I have used the GH browser successfully on a number of BAM files. Now I have a genome in CRAM format and I can't seem to do anything with it. GH apparently won't load it. I can not understand the unix tools that may be available for converning files. Is there any simple way around this problem? Is there any way to make GH recognize and load a CRAM file? Maybe I don't have the most recent version?Whit AtheyFri, 07 Aug 2020 17:57:06 +0000http://answers.goldenhelix.com/question/479/http://answers.goldenhelix.com/question/464/to-implement-refseq-genome/ In Italian laboratory we usually perform bacteria WGS, so i search a valid tool to display BAM file. In the past i used GenomeBrowse for human genome analysis and I have find this tool very useful, but at the moment the brawser collect few bacterial genome. Do you think that is possible add new refseq for bacteria genome analysis?Angelica BiancoMon, 29 Apr 2019 05:32:04 +0000http://answers.goldenhelix.com/question/464/http://answers.goldenhelix.com/question/488/dark-reads-in-pile-up-track/When displaying some tracks in the browser, in the wide-zoom view, some reads in the pile-up track appear dark (almost black). The color of the pile-up track quickly shifts from the ususal green to black in some areas and I can't identify a reason for it, since the underlaying reads don't seem to have consistent differences in mapping quality or amount of missmatches. Thanks very much in advance!Lucas Michel TodoMon, 12 Apr 2021 08:01:18 +0000http://answers.goldenhelix.com/question/488/http://answers.goldenhelix.com/question/484/reads-fragments/ hello How I can see these fragments/reads from the sequencing? I have 20x sequenced, so there are average 20 reads. But how can see them?Christian AltorferMon, 07 Dec 2020 05:52:25 +0000http://answers.goldenhelix.com/question/484/http://answers.goldenhelix.com/question/482/why-is-the-coverage-track-not-grey-anymore/When opening BAM files in Golden helix genome browse 3.0.0 my coverage track is no longer grey (only colored if there is a variant present). Now, the bases are colored like in the reference sequence track (green, yellow, red and blue) and my variants are shown in the coverage track and no longer the pile-up track as it used to. Is this a new setting, and can I set it back?! The software is useless to me now, with these new settings. Signe NeldeborgTue, 08 Sep 2020 06:58:02 +0000http://answers.goldenhelix.com/question/482/http://answers.goldenhelix.com/question/475/display-phasing-in-vcfs/Hey there, When I load a VCF into GenomeBrowser, it nicely displays all my variants for all my samples. However, if I load a VCF with phased haplotypes and Sample1 has genotype 0|1 at Variant1 and 2|0 at Variant2 (a multiallelic variant), then it seems that Sample1 is displayed as 0|1, 0|2 in the browser, not 0|1, 2|0. Is there any option that, for phased VCFs, will force alleles in the same row for a sample to always be of the same haplotype? Thanks, JonathanJ MWed, 18 Dec 2019 16:25:34 +0000http://answers.goldenhelix.com/question/475/http://answers.goldenhelix.com/question/473/when-i-try-to-add-a-bam-file-to-a-project-that-already-has-several-bam-files-i-get-this-bam-file-truncated-error-code-3-what-causes-this-error-i-see/ This error occurred during the computation of the BAI index.Whit AtheyThu, 14 Nov 2019 21:22:57 +0000http://answers.goldenhelix.com/question/473/http://answers.goldenhelix.com/question/470/current-filters-hide-all-data-sources/I wish to upload bam files to align to the human ref seq (GRCh37). The local folder contains fastq.bam + fastq.bam.bai files, where the former has the blue golden helix logo. Yet the browser is unable to recognize these files and returns the above warning. The filter is set to 'any type'. Should the these bam files be converted to a more suitable format for Golden Helix? If so why, do they show the Golden Helix logo?Alex MorrisWed, 11 Sep 2019 09:18:06 +0000http://answers.goldenhelix.com/question/470/http://answers.goldenhelix.com/question/469/i-have-a-folder-of-bam-files-i-wish-to-open-with-gb-gh/ I have looked at a youtube video but the add drop down menus are missing fom this GBAlex MorrisWed, 11 Sep 2019 08:50:01 +0000http://answers.goldenhelix.com/question/469/http://answers.goldenhelix.com/question/465/how-do-i-add-field-to-style-by-option-in-controls/I need to style the color of points I'm plotting by a field in my tsf file. However, the field is not listed in the drop-down menu provided in the style tab of the controls menu.Jeremy SchroederWed, 12 Jun 2019 16:26:54 +0000http://answers.goldenhelix.com/question/465/http://answers.goldenhelix.com/question/466/export-information-on-sequence-reads/ Hi, We are studying the rate of de novo mutagenesis after genetic engineering. We have deep-sequenced a target region of 2kb and are interested to know how many mutations have been generated and at what percentage. I understand we can click on a specific nucleotide and obtain from the data console the read information. Is there a way that I can obtain the collective read information for each nucleotide of the whole 2kb region without having to click on each of them one by one?Yan LiMon, 24 Jun 2019 10:55:15 +0000http://answers.goldenhelix.com/question/466/http://answers.goldenhelix.com/question/461/converting-23andme-raw-data/ Greetings, I am attempting to convert my raw 23andMe v4 raw data using the steps outlined by Jeffrey Moore on his YouTube channel. In the conversion wizard preview, the genotypes field is missing. Unfortunately I am unable to post a screen shot because this is my first post to this community. In the Preview box, I see all fields except genotypes. To clarify, the input fields I see are: Ref/Alt, Identifier, Reference, Alternates, 0/1 Genotypes, Samples. The missing field is Genotypes. I don't know if this normal since the video was posted in 2015 and the version has since changed, or if this is due to a problem parsing the file. Thank you. Frederick KarayanSat, 20 Apr 2019 09:03:55 +0000http://answers.goldenhelix.com/question/461/http://answers.goldenhelix.com/question/460/gautil-coverage-failing-to-identify-genome-assembly/I am trying to use gautil coverage on my Mac to produce the coverage graphs (and zoomed out pile-up) prior to loading .bam files into GenomeBrowse, as if I have a lot of .bam files and if they are only processed one by one in GenomeBrowse GUI, it takes a very long time. I am running the following command from within the GenomeBrowse 'Tools' folder where gautil is located: ./gautil coverage /Users/username/examplefolder/INPUT.bam --refFolder="/Users/username/Library/Application Support/Golden Helix/Common Data/Annotations/" And the output I receive is as follows: Unable to find reference sequence source for build: Ran into errors: Unable to match data in this source with an existing reference sequence. Reference sequence must have matching chromosome names and lengths. It seems to me that gautil is unable to identify which genome assembly my alignments are to in my .bam. When I drag and drop the same .bam file into GenomeBrowse it is able to do the computation fine, so I am not sure what the problem is. I have tried using different .bam files and also I have tried specifying the .tsf reference sequence file path directly instead of specifying the path to the folder containing it, but these didn't work. A colleague of mine seems to be doing the same thing as I am doing on Windows but having it work, so I am wondering whether this is a Mac-specific issue, or whether I am making some mistake in replicating his method.Haskan KayaWed, 27 Feb 2019 18:14:04 +0000http://answers.goldenhelix.com/question/460/http://answers.goldenhelix.com/question/459/scerevisiae-genome/Hi, I cannot show *Saccharomyces cerevisiae* genome on the GenomeBrowse. Is there any available data about *S.cerevisiae* in GenemoBrowse or can we add fasta format of the DNA of *S.cerevisiae*? Thanks in advance.Koray MalciWed, 23 Jan 2019 10:19:26 +0000http://answers.goldenhelix.com/question/459/http://answers.goldenhelix.com/question/452/why-does-genomebrowse-terminate-when-clicking-to-plot-icon/I have been using GenomeBrowse 3.0.0 for several months in Ubuntu 16.04 LTS operating system. It worked well until last week. I can view anything in an existing project even now. However, when I click at the Plot icon to add new samples to a project, it exits with the following message: terminating Aborted (core dumped) I re-installed GenomeBrowse 3.0.0. Unfortunately, it failed to help. Can you tell me the reason for that behavior? What should I do to fix that problem? Thank you in advance for your help! Tibor VaszkóMon, 10 Sep 2018 04:53:43 +0000http://answers.goldenhelix.com/question/452/http://answers.goldenhelix.com/question/168/hgmd-integration/We have purchased HGMD and was wondering how we can get a track into GenomeBrowse.Erin HedlundTue, 02 Jul 2013 16:24:19 +0000http://answers.goldenhelix.com/question/168/http://answers.goldenhelix.com/question/451/cnv-breakpoints-in-read-pile-up/Hi, I have a very rare example of a sub-exonic duplication, confirmed in the clinic. A different IGV-like tool enable the detection of break-points by showing miss-aligned read tails spanning the break-point. On the other hand, GB does not enable this break-point detection as the reads seem to be clipped off at the break-point and onward (where the sequence is miss-aligned). I've tried playing with the filters but it doesn't seem to help. The other break-point same story. Is there a way to enable GB visualise the miss-aligned read tails for break-point detection? *I wanted to upload and share the snippet but need 10 points to upload pictures (?) Michael VolodarskyTue, 17 Jul 2018 11:02:15 +0000http://answers.goldenhelix.com/question/451/http://answers.goldenhelix.com/question/450/command-line-for-capturing-snapshots/ Hi, Could I control the GenomeBrowse to navigate a specific coordinate and capture alignment snapshots by command-line mode in Ubuntu? Do you have tutorial to demo that? Thanks, KWKevin WuTue, 17 Jul 2018 03:45:11 +0000http://answers.goldenhelix.com/question/450/http://answers.goldenhelix.com/question/448/error-logging-into-genomebrowse-with-ssh-handshake-failed/ When logging in, I get a "SSH handshake failed" message!Gabe RudyWed, 09 May 2018 13:26:39 +0000http://answers.goldenhelix.com/question/448/http://answers.goldenhelix.com/question/447/how-to-convert-column-type-when-there-are-too-many-columns/ Hi, I ave more than 700000 columns of genotyping data that I need to do analysis on, But in every step I come to this error: you need active columns which are genotypic. My data were type C when I imported them into SVS. I tried to change the column type to G in the edit tab, but it is only done one by one and imagine 700000 columns!! Is there any way I can convert all my columns into Genotype type? Or Is there anything I can change when importing the data to get the output spreadsheet with G type? my original genotyping data is available as text, csv and excell. Thank youSahar DehghanThu, 01 Mar 2018 01:57:56 +0000http://answers.goldenhelix.com/question/447/http://answers.goldenhelix.com/question/446/how-can-i-know-the-minimum-coverage-of-a-sequenced-region/ Hi, I have sequenced some genes of *P. falciparum* genome using MiSeq. Is there a tool to calculate **minimum coverage**? Also, in the console, what does **Bin Size** refer to?Rebecca SmithWed, 24 Jan 2018 08:33:04 +0000http://answers.goldenhelix.com/question/446/http://answers.goldenhelix.com/question/445/converting-gtf-using-custom-genome/ Hi I have converted a new custom genome from .fa to .tsf. Next when I convert the respective GTF file, I do not get the new genome under the genome options. I only get a list of the standard genomes and of course my GTF doesn't match any of those. Using GenomeBrowse 2.1.2. Please advice. Thanks.r fTue, 23 Jan 2018 04:44:29 +0000http://answers.goldenhelix.com/question/445/http://answers.goldenhelix.com/question/444/any-way-to-import-an-oreganno-track/I'd like to be able to view ORegAnno regulatory information in GenomeBrowse, but it is not listed as a standard public track. Has anyone come up with a way to display these? Dan CohnMon, 08 Jan 2018 13:16:41 +0000http://answers.goldenhelix.com/question/444/