Moderator: John Marshall
John Marshall ♦ 2.1k
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- Glasgow, Scotland
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- jomarnz
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- Joined:
- 8 years, 8 months ago
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Posts by John Marshall
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0
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75
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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 days ago by
John Marshall ♦ 2.1k
1
vote
1
answer
77
views
1
answers
Comment:
C: Bcftools filter error
... This may be the recently fixed [bcftools issue #1266](https://github.com/samtools/bcftools/issues/1266). ...
written 9 days ago by
John Marshall ♦ 2.1k
2
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3
answers
110
views
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 13 days ago by
John Marshall ♦ 2.1k
1
vote
1
answer
222
views
1
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... 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 4 weeks ago by
John Marshall ♦ 2.1k
6
votes
1
answer
222
views
1
answers
... No. The BAI format is described in §5.2 of [SAMv1.pdf](http://samtools.github.io/hts-specs/SAMv1.pdf) and does not contain the chromosome names or lengths. Instead it merely identifies reference sequences by their index, 0 <= n < n_ref, in the corresponding BAM file's (binary) header.
The CSI ...
written 4 weeks ago by
John Marshall ♦ 2.1k
0
votes
0
answers
135
views
0
answers
... The real question is what program or instrument has produced these reads with unusual names like `read1_1` or `read1.1`. ...
written 10 weeks ago by
John Marshall ♦ 2.1k
1
vote
2
answers
162
views
2
answers
... `samtools bam2fq` is a synonym for `samtools fastq`. ...
written 11 weeks ago by
John Marshall ♦ 2.1k
4
votes
1
answer
182
views
1
answers
... Snakemake doesn't know what strains you want it to make `dbs/*-db` for. You could tell it on the command line, i.e., specify the targets concretely:
$ snakemake -n --snakefile snakefile.txt --cores 2 -p dbs/A-db dbs/B-db dbs/C-db
or you can add an umbrella rule that fans out to all the strains ...
written 4 months ago by
John Marshall ♦ 2.1k
1
vote
1
answer
199
views
1
answers
Comment:
C: BAM file output
... It would appear that whatever the tool you've used to display the contents is, it's rather unusually chosen to write out the individual base qualities numerically — instead of the SAM file's native QUAL field, an ASCII-encoded string of base qualities. ...
written 7 months ago by
John Marshall ♦ 2.1k
2
votes
3
answers
315
views
3
answers
... Even better and easier to use a tool that understands what's in a FASTA file. For example, index the FASTA file using
samtools faidx yourgenome.fa
and add up the second column of the resulting *yourgenome.fa.fai* file. ...
written 8 months ago by
John Marshall ♦ 2.1k
Latest awards to John Marshall
Teacher
4 weeks ago,
created an answer with at least 3 up-votes.
For A: sam header is not recognized by awk?
Scholar
4 weeks ago,
created an answer that has been accepted.
For A: Need help interpreting gdb backtrace from a SAMtools segmentation default (or he
Good Answer
4 weeks ago,
created an answer that was upvoted at least 5 times.
For A: Question about sam flags.
Teacher
4 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: Need help interpreting gdb backtrace from a SAMtools segmentation default (or he
Scholar
9 months ago,
created an answer that has been accepted.
For A: Need help interpreting gdb backtrace from a SAMtools segmentation default (or he
Teacher
9 months ago,
created an answer with at least 3 up-votes.
For A: sam header is not recognized by awk?
Good Answer
11 months ago,
created an answer that was upvoted at least 5 times.
For A: Question about sam flags.
Scholar
11 months ago,
created an answer that has been accepted.
For A: SAMtools-1.2 sort options documentation
Teacher
11 months ago,
created an answer with at least 3 up-votes.
For A: sam header is not recognized by awk?
Teacher
12 months ago,
created an answer with at least 3 up-votes.
For A: sam header is not recognized by awk?
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14 months ago,
created an answer that has been accepted.
For A: SAMtools-1.2 sort options documentation
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14 months ago,
created 100 posts.
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15 months ago,
created a post with more than 5 votes.
For A: Duplicate @Sq Lines In Sam File Header
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created an answer that was upvoted at least 5 times.
For A: Duplicate @Sq Lines In Sam File Header
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
17 months ago,
created an answer with at least 3 up-votes.
For A: sam header is not recognized by awk?
Scholar
17 months ago,
created an answer that has been accepted.
For A: SAMtools-1.2 sort options documentation
Good Answer
23 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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23 months ago,
created a post with more than 5 votes.
For A: Tool for random access to indexed BAM files in S3?
Scholar
23 months ago,
created an answer that has been accepted.
For A: SAMtools-1.2 sort options documentation
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