Moderator: John Marshall
John Marshall ♦ 1.5k
- Reputation:
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- Glasgow, Scotland
- Twitter:
- jomarnz
- Last seen:
- 12 hours ago
- Joined:
- 7 years, 5 months ago
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Posts by John Marshall
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... 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 Marshall ♦ 1.5k
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102
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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 Marshall ♦ 1.5k
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... 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 Marshall ♦ 1.5k
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... 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 Marshall ♦ 1.5k
2
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1
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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 Marshall ♦ 1.5k
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... 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 Marshall ♦ 1.5k
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1.1k
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1
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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 Marshall ♦ 1.5k
1
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1
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1.1k
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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 Marshall ♦ 1.5k
1
vote
1
answer
571
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1
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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 Marshall ♦ 1.5k
0
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3
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480
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3
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... 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 Marshall ♦ 1.5k
Latest awards to John Marshall
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6 weeks ago,
created an answer that has been accepted.
For A: SAMtools-1.2 sort options documentation
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6 weeks ago,
created an answer with at least 3 up-votes.
For A: sam header is not recognized by awk?
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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?
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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?
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7 months ago,
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For A: Tool for random access to indexed BAM files in S3?
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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,
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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?
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8 months ago,
created an answer that has been accepted.
For A: SAMtools-1.2 sort options documentation
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9 months ago,
created an answer with at least 3 up-votes.
For A: sam header is not recognized by awk?
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17 months ago,
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For A: sam header is not recognized by awk?
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20 months ago,
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For A: sam header is not recognized by awk?
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received more than 100 upvotes.
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2.1 years ago,
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2.4 years ago,
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2.5 years ago,
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2.5 years ago,
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For A: Velvet-SC installation/compilation issues
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2.5 years ago,
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For C: SAM file: same reads ID, slightly different sequence
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