User: gubrins

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gubrins60
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gubrins
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Posts by gubrins

<prev • 83 results • page 1 of 9 • next >
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Convert vcf to eigenstrat
... Heys, I'm working on population genomics and I would like to convert my vcf file to eigenstrat. I've been looking for internet but I did not find any common software that does it (maybe I missed some?) and I tried to run several scripts from github but it did not work. Anybody can help me on this? ...
vcf eigenstrat written 3 days ago by gubrins60
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Multisample BAM file
... Heys, I'm trying to run GATK on some BAM files I got. When I try, I obtain this error message: > A USER ERROR has occurred: Argument emit-ref-confidence has a bad value: Can only be used in single sample mode currently. Use the --sample-name argument to run on a single sample out of a multi-sam ...
snp calling bam samtools written 23 days ago by gubrins60 • updated 23 days ago by vareenjuriya0
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Answer: A: MarkDuplicates of a queryname sorted bam more expensive than a coordinate sorted
... I imagine this post answers your question: https://github.com/broadinstitute/picard/issues/1119 "When the input is coordinate-sorted, unmapped mates of mapped records and supplementary/secondary alignments are not marked as duplicates. However, when the input is query-sorted (actually query-grouped ...
written 5 weeks ago by gubrins60
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Comment: C: Filter per tile quality
... I tried to filter them with filterbytile but it did not improve the results... Luckily I have the reference genome, thanks for your help! :) ...
written 6 weeks ago by gubrins60
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Comment: C: Filter per tile quality
... thanks, did you also check this one? Is not updating properly in the first message: ![picture 2][1] [1]: https://i.ibb.co/Jn4R49J/per-tile-quality.png ...
written 6 weeks ago by gubrins60
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Comment: C: Filter per tile quality
... is it okey now? thanks for the message! ...
written 6 weeks ago by gubrins60
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Filter per tile quality
... Heys, I'm working with whole-genome sequencing data of a non-model organism. I ran the FastQC for the quality control of the data and I found faliures both in adapter content and tile's quality. Adapter content is not an issue anymore, but I'm struggling with per tile sequence quality. I tried to f ...
tile genomes fastqc written 6 weeks ago by gubrins60
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Comment: C: How to filter fastq paired-end reads based on Per Tile Sequence Quality
... I'm also interested!! ...
written 7 weeks ago by gubrins60
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Comment: C: genome coverage visualization
... Thanks again for your great answer! Although is not exactly what I need right now, I'm sure I'll use it in the future for checking the coverage of specific regions of my interest! Really interesting package, thanks again! ...
written 7 weeks ago by gubrins60
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Comment: C: How to plot coverage and depth statistics of a bam file
... does it work if you are not interested into knowing the coverage per regions of interest but for all the data? ...
written 7 weeks ago by gubrins60

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Supporter 8 months ago, voted at least 25 times.

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