Moderator: John Marshall

gravatar for John Marshall
John Marshall1.5k
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Glasgow, Scotland
Twitter:
jomarnz
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12 hours ago
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7 years, 5 months ago
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Posts by John Marshall

<prev • 95 results • page 1 of 10 • next >
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Comment: C: Type checker error with bedtools intersect
... That's not a BAM file. If you showed us the command used to make it, we would be able to guess at what format it actually is. ...
written 3 days ago by John Marshall1.5k
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Comment: C: VCF INFO interpretation
... Your go-to link for VCF should be the [4.3 spec](https://samtools.github.io/hts-specs/VCFv4.3.pdf). The differences between 4.1/4.2/4.3 are fairly minor for people examining data in them, and lots of things common to all three are best described in the latest specification. ...
written 19 days ago by John Marshall1.5k
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Comment: C: how to compute the insert size in SAM file
... The 4486 pair are an "outie" mapping — the read at the lower coordinate is the reversed one. So you would have to tell us more about your sequencing protocol for us to venture an opinion on why this has been marked as a proper pair and had an insert size calculated at all. Indeed: Which tool produc ...
written 5 weeks ago by John Marshall1.5k
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Answer: A: How does bedtools bamtobed calculate end position
... Bamtobed is using the CIGAR string to measure each read length in terms of *positions matched along the reference sequence*. For example, for the first read, r001: r001 163 ref 7 30 8M4I4M1D3M …etc… The CIGAR string can be used to reconstruct the mapping of the read ...
written 6 weeks ago by John Marshall1.5k
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Answer: A: Bam file MC tag as integer
... > ID:bamstreamingmarkduplicates Older versions of the biobambam tools used an integer `MC:i` tag to communicate duplicate marking statistics from one part of biobambam to another. More recent versions use a more appropriate [`mc:i` tag and strip out an integer `MC` if there is one](https://gitl ...
written 11 weeks ago by John Marshall1.5k
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Answer: A: samtools " Assertion `iter->curr_off == iter->off[iter->i].v' failed". "
... That error message indicates that you are using samtools 0.1.19. This was released almost six years ago, and still using it is a problem in itself… ...
written 4 months ago by John Marshall1.5k
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Comment: C: install Primer3 on Ubuntu
... Do you conda advocates ever get bored of saying “have you tried conda?”? What would be useful would be if you said “This works in bioconda because we have invented an unofficial 2.4.1a release that includes a few post-2.4.0 commits from upstream primer3, notably a fix for this *thal.c:429* problem. ...
written 5 months ago by John Marshall1.5k
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Comment: C: install Primer3 on Ubuntu
... This worked because you are now building git HEAD rather than the 2.4.0 release. The *thal.c:429* et al errors in the original question were bugs that were fixed in [May 2018](https://github.com/primer3-org/primer3/commit/2a04aa2e11e3c7a7d91c208b842a76754a840c87#diff-f8db35be2213e9f267cb700f904a89b7 ...
written 5 months ago by John Marshall1.5k
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Comment: C: Review of the CIGAR string format
... `=` and `X` appeared in SAM v1.3 in July 2009, in and the surrounding thread. ...
written 7 months ago by John Marshall1.5k
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Answer: A: How to use samtools tview goto with long reference sequence name
... Sadly this text entry box is too narrow for unfortunate contigs named via UUIDs. See PR [samtools/samtools#968](https://github.com/samtools/samtools/pull/968). In the meantime, there is a workaround to jump to the position you're after using a vanilla samtools tview build: the goto command accepts ...
written 7 months ago by John Marshall1.5k

Latest awards to John Marshall

Scholar 6 weeks ago, created an answer that has been accepted. For A: SAMtools-1.2 sort options documentation
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Tool for random access to indexed BAM files in S3?
Appreciated 7 months ago, created a post with more than 5 votes. For A: Tool for random access to indexed BAM files in S3?
Scholar 7 months ago, created an answer that has been accepted. For A: SAMtools-1.2 sort options documentation
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Appreciated 7 months ago, created a post with more than 5 votes. For A: Tool for random access to indexed BAM files in S3?
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: SAM file: same reads ID, slightly different sequence
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Scholar 8 months ago, created an answer that has been accepted. For A: SAMtools-1.2 sort options documentation
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Question about sam flags.
Scholar 21 months ago, created an answer that has been accepted. For A: Question about sam flags.
Scholar 23 months ago, created an answer that has been accepted. For A: Question about sam flags.
Guru 2.0 years ago, received more than 100 upvotes.
Scholar 2.1 years ago, created an answer that has been accepted. For A: Velvet-SC installation/compilation issues
Good Answer 2.4 years ago, created an answer that was upvoted at least 5 times. For A: Question about sam flags.
Scholar 2.5 years ago, created an answer that has been accepted. For A: Velvet-SC installation/compilation issues
Scholar 2.5 years ago, created an answer that has been accepted. For A: Velvet-SC installation/compilation issues
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Question about sam flags.
Commentator 2.5 years ago, created a comment with at least 3 up-votes. For C: SAM file: same reads ID, slightly different sequence
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Question about sam flags.

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