Moderator: John Marshall

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John Marshall2.1k
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Glasgow, Scotland
Twitter:
jomarnz
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8 years, 8 months ago
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Posts by John Marshall

<prev • 120 results • page 1 of 12 • next >
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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 Marshall2.1k
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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 9 days ago by John Marshall2.1k
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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 13 days ago by John Marshall2.1k
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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 4 weeks ago by John Marshall2.1k
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Answer: A: Does bai file contain chromosome names and their lengths?
... 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 Marshall2.1k
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Comment: C: BWA mem paired end read name errors
... 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 Marshall2.1k
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Comment: C: Does BWA MEM understand paired-end suffixes? /2 in a single FASTQ file?
... `samtools bam2fq` is a synonym for `samtools fastq`. ...
written 11 weeks ago by John Marshall2.1k
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Answer: A: My snakefile won't run because of wildcards-please help!
... 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 Marshall2.1k
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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 Marshall2.1k
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Answer: A: How to properly measure the length of a reference genome
... 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 Marshall2.1k

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
Appreciated 4 weeks ago, created a post with more than 5 votes. For A: Question about sam flags.
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.
Appreciated 11 months ago, created a post with more than 5 votes. 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?
Scholar 14 months ago, created an answer that has been accepted. For A: SAMtools-1.2 sort options documentation
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Appreciated 15 months ago, created a post with more than 5 votes. For A: Duplicate @Sq Lines In Sam File Header
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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
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Scholar 23 months ago, created an answer that has been accepted. For A: SAMtools-1.2 sort options documentation

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