Moderator: John Marshall

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John Marshall2.2k
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Glasgow, Scotland
Twitter:
jomarnz
Last seen:
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9 years ago
Email:
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Posts by John Marshall

<prev • 126 results • page 1 of 13 • next >
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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 Marshall2.2k
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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 If the OP fixes this libcrypto problem they'll have a working samtools executable, but it'll still be a massively out-of-date version of samtools!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 Marshall2.2k
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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[limitation in conda](https://github.com/bioconda/bioconda-recipes/issues/24199): conda has given you an out of date version of samtools.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 Marshall2.2k
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Comment: C: How to fix minimap2 -> samtools sort error (samtools sort: truncated file. Abort
... 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 Marshall2.2k
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Answer: A: How can I get the uncompressed size of a BGZIP file ?
... 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 Marshall2.2k
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Answer: A: How to filter out chromosome regions from a .bam file
... `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 Marshall2.2k
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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 Marshall2.2k
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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 Marshall2.2k
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Answer: A: bedtools sort doesn't properly sort
... 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 Marshall2.2k
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Comment: C: Does bai file contain chromosome names and their lengths?
... 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 Marshall2.2k

Latest awards to John Marshall

Teacher 6 days ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Scholar 10 weeks ago, created an answer that has been accepted. For A: Need help interpreting gdb backtrace from a SAMtools segmentation default (or he
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Question about sam flags.
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Question about sam flags.
Scholar 5 months ago, created an answer that has been accepted. For A: Need help interpreting gdb backtrace from a SAMtools segmentation default (or he
Appreciated 5 months ago, created a post with more than 5 votes. For A: Question about sam flags.
Teacher 5 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 12 months ago, created an answer that has been accepted. For A: Need help interpreting gdb backtrace from a SAMtools segmentation default (or he
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Scholar 13 months ago, created an answer that has been accepted. For A: Need help interpreting gdb backtrace from a SAMtools segmentation default (or he
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Question about sam flags.
Appreciated 15 months ago, created a post with more than 5 votes. For A: Question about sam flags.
Scholar 15 months ago, created an answer that has been accepted. For A: SAMtools-1.2 sort options documentation
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Scholar 18 months ago, created an answer that has been accepted. For A: SAMtools-1.2 sort options documentation
Centurion 18 months ago, created 100 posts.
Good Answer 19 months ago, created an answer that was upvoted at least 5 times. For A: Duplicate @Sq Lines In Sam File Header
Appreciated 19 months ago, created a post with more than 5 votes. For A: Duplicate @Sq Lines In Sam File Header
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Scholar 19 months ago, created an answer that has been accepted. For A: SAMtools-1.2 sort options documentation
Scholar 21 months ago, created an answer that has been accepted. For A: SAMtools-1.2 sort options documentation

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