Moderator: finswimmer

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finswimmer6.2k
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Posts by finswimmer

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Comment: C: Installing samtools from sourceforge
... With [conda][1] you can easily install any version you like. [1]: https://www.biostars.org/p/335903/ ...
written 21 hours ago by finswimmer6.2k
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Comment: C: Installing samtools from sourceforge
... Hello, Why? [You] [1] [were][2] [told][3] to update to the newest version. fin swimmer [1]: https://www.biostars.org/p/343591/#343612 [2]: https://www.biostars.org/p/343591/#343770 [3]: https://www.biostars.org/p/343591/#343833 ...
written 23 hours ago by finswimmer6.2k
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Comment: C: unable to load quant.sf files
... Hello https://www.biostars.org/u/49459/ , Please use the formatting bar (especially the `code` option) to present your post better. I've done it for you this time. Thank you! ...
written 1 day ago by finswimmer6.2k
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Answer: A: Which human reference genome should I use?
... **Why one must masked the PAR region for alignment?** Let's do some biology to understand this. During meiosis there is a process call crossing over. During this parts of homologues chromosomes are exchange between each other. But what about the case of X and Y chromosome as they don't build a reg ...
written 1 day ago by finswimmer6.2k
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Comment: C: How to ignore truncation error with PySam?
... Hello https://www.biostars.org/u/28277/ , - Why do you want to do this? - The `ignore_truncation` isn't do what you are thinking. From the [manual][1]: `Issue a warning, instead of raising an error if the current file appears to be truncated due to a missing EOF marker. Only applies to bgzipped for ...
written 1 day ago by finswimmer6.2k
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Comment: C: How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
... Hello https://www.biostars.org/u/42413/ , again: Update the version! I edited my commands as I missed the `view` in the `bcftools`command. And as https://www.biostars.org/u/4407/ says the output of `mpileup` must be in a `bcf`format. fin swimmer ...
written 1 day ago by finswimmer6.2k
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Comment: C: How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
... Yes, you're right. Fixed it. ...
written 1 day ago by finswimmer6.2k
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Comment: C: Bedtools intersect alternatives available
... That's a better description about the problem you are trying to solve. Some ideas: - Use `tabix` to index your `bed` file. Doing this you can have random access to given regions. - Think about splitting your regions you want to intersect with and use `gnu parallel` fin swimmer ...
written 1 day ago by finswimmer6.2k
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Comment: C: Bedtools intersect alternatives available
... It depens on what you want to "intersect". ...
written 1 day ago by finswimmer6.2k
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Comment: C: How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
... I think your problem is understanding what is mpileup for. I will try to explain it: Using samtools/bcftools for variant discovering is a 2-step process. In the first step - called mpileup - samtools will generate information about each single position of the reference sequence. This contains how ...
written 1 day ago by finswimmer6.2k

Latest awards to finswimmer

Scholar 2 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Scholar 5 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Scholar 7 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Appreciated 7 days ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Scholar 7 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Appreciated 8 days ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Scholar 8 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Commentator 13 days ago, created a comment with at least 3 up-votes. For A: sam file error
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Teacher 18 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
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Commentator 5 weeks ago, created a comment with at least 3 up-votes. For A: sam file error
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Scholar 6 weeks ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
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Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: Extract SNPs from VCFfile located in genes based on GFF file information

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