Moderator: John Marshall
John Marshall ♦ 2.2k
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- Twitter:
- jomarnz
- Last seen:
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- Joined:
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Posts by John Marshall
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Comment:
C: Samtools Faidx Error Message
... This is (for now) fixed; plain `conda create -n myenv samtools` will give you an up-to-date version of samtools. ...
written 11 days ago by
John Marshall ♦ 2.2k
0
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Comment:
C: Samtools Faidx Error Message
... That's working around the effect, rather than working around the cause. If the OP fixes this libcrypto problem they'll have a working samtools executable, but it'll still be a massively out-of-date version of samtools!
(For when you do want to reproduce an old analysis with an old samtools, the way ...
written 15 days ago by
John Marshall ♦ 2.2k
1
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Answer:
A: Samtools Faidx Error Message
... This is a currently-existing [limitation in conda](https://github.com/bioconda/bioconda-recipes/issues/24199): conda has given you an out of date version of samtools. See also [this Twitter thread](https://twitter.com/jomarnz/status/1293515960981368838).
At the moment, you should work around this b ...
written 15 days ago by
John Marshall ♦ 2.2k
0
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... The htslib/samtools “QNAMEs limited to 252 characters instead of 254” bug was fixed in 1.10.
The absence of an additional `[E::sam_parse1] query name too long` error message is also indicative that this is not the problem. ...
written 4 weeks ago by
John Marshall ♦ 2.2k
2
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2
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228
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2
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... Each block of a BGZF file is itself a valid GZIP file. So you can calculate the overall uncompressed size as the total of all those size entries recorded in the last four bytes of each GZIP member file.
It remains to find the end of each BGZF block, but fortunately each block's header contains a BC ...
written 8 weeks ago by
John Marshall ♦ 2.2k
5
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... `samtools view -U file` will output reads not selected by filters to `file`. This does not apply to regions specified on the command line (after the input file name) or with `-M`, as using the index to jump to the specified regions is separate from “filtering the reads” — however it does apply to `- ...
written 10 weeks ago by
John Marshall ♦ 2.2k
0
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2
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243
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2
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Comment:
C: Sort a bed file
...
Hello kmkdesilva!
Questions similar to yours can already be found at:
bedtools sort doesn't properly sort
We have closed your question to allow us to keep similar content in the same thread.
If you disagree with this please tell us why in a reply below. We'll be happy to talk a ...
written 4 months ago by
John Marshall ♦ 2.2k
1
vote
1
answer
214
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1
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Comment:
C: Bcftools filter error
... This may be the recently fixed [bcftools issue #1266](https://github.com/samtools/bcftools/issues/1266). ...
written 4 months ago by
John Marshall ♦ 2.2k
3
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3
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236
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3
answers
... The chromosomes have been sorted alphabetically by default.
If you have e.g. a .fai file that lists the chromosomes in the natural order that you would prefer, you should use it with the [`bedtools sort -g` option](https://bedtools.readthedocs.io/en/latest/content/tools/sort.html) to specify your p ...
written 4 months ago by
John Marshall ♦ 2.2k
1
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1
answer
310
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1
answers
... I am at present one of the editors of the SAM specification and a former SAMtools maintainer. But in fact this answer, like any other, should be accepted as correct or not based on **its own merits**, not its author — I included links to the various specifications precisely so that the claims made c ...
written 5 months ago by
John Marshall ♦ 2.2k
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6 days ago,
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For A: sam header is not recognized by awk?
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10 weeks ago,
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For A: Need help interpreting gdb backtrace from a SAMtools segmentation default (or he
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For A: Question about sam flags.
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For A: sam header is not recognized by awk?
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For A: sam header is not recognized by awk?
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For A: Need help interpreting gdb backtrace from a SAMtools segmentation default (or he
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For A: sam header is not recognized by awk?
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For A: SAMtools-1.2 sort options documentation
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For A: SAMtools-1.2 sort options documentation
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For A: SAMtools-1.2 sort options documentation
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