User: John Marshall

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John Marshall1.2k
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Glasgow, Scotland
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jomarnz
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6 years, 5 months ago
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Posts by John Marshall

<prev • 71 results • page 1 of 8 • next >
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Comment: C: BWA MEM Supplementary Tag Position (0 or 1 based)
... It is indeed a 1-based coordinate, and this has now been clarified in the spec. Thanks for bringing this to our attention. ...
written 19 days ago by John Marshall1.2k
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Comment: C: sequence and quality are inconsistent
... You may have installed samtools 1.3 (which is also somewhat out of date at this point), but if it is printing out "[samopen] SAM header is present" then you are actually using samtools 0.1.18 or thereabouts. Check your $PATH, because you're not using the version of samtools that you think you are. ...
written 3 months ago by John Marshall1.2k
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Comment: C: sequence and quality are inconsistent
... 1. You are using a prehistoric version of samtools. 2. Did you consider looking at line 31099973? ...
written 3 months ago by John Marshall1.2k
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Comment: C: samtools pileup format: insertions and deletions' quality
... Please don't cross-post with the [mailing list](https://sourceforge.net/p/samtools/mailman/message/36245398/) — pick one or the other. ...
written 3 months ago by John Marshall1.2k
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Answer: A: samtools pileup format: insertions and deletions' quality
... You can answer these questions yourself by experimenting with a simple SAM file like the following: @SQ SN:chr3 LN:1000000 foo 0 chr3 70000 20 4M * 0 0 ATGC abcd bar 0 chr3 80000 20 2M2I2M * 0 0 AATGCC abcdef baz 0 chr3 90000 20 2M2D2M * 0 0 ATGC abcd Look at the output of `samtoo ...
written 3 months ago by John Marshall1.2k
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Answer: A: SAMTOOLS SORT eeor
... The strange hieroglyphics are your sorted output, and the nine files you saw are temporary files used during sorting. Time to reread the manual: > The sorted output is written to standard output by default, or to the specified file (out.bam) when **-o** is used. This command will also c ...
written 5 months ago by John Marshall1.2k
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Answer: A: Samtools mpileup output: missing fields?
... The article you're looking at is an ancient web page discussing the old **pileup** format, which is similar to but a simplified version of **mpileup** format, which replaced the old format with the arrival of the `samtools mpileup` command quite some years ago. Instead you should look at the (admit ...
written 9 months ago by John Marshall1.2k
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Answer: A: BAM Index Chunks
... `chunk_beg`..`chunk_end` is the range of file offsets within the BAM file telling you where in the file the records are. There can be several chunks because the read records within a bin are not necessarily all contiguous in the BAM file — there can be reads from other bins interspersed with them. ...
written 9 months ago by John Marshall1.2k
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Answer: A: faidx implementation with C++
... Read , which discusses the format of _.fai_ files and how they are used to index well-formatted FASTA files. Working from this will be clearer than working from the implementation in HTSlib, and when you are more familiar with it the HTSlib/Samtools implementation may make a bit more sense. ...
written 10 months ago by John Marshall1.2k
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Comment: C: what should a SAM/BAM record contain when there are no quality scores
... There's also text about this in §1.4 talking specifically about SAM's QUAL: “This field can be a ‘*’ when quality is not stored”. Incidentally, if the text about “a sequence of 0xFF if absent” is on p16 of your copy of the SAM specification, then you have a somewhat out of date specification from b ...
written 10 months ago by John Marshall1.2k

Latest awards to John Marshall

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?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Question about sam flags.
Scholar 9 months ago, created an answer that has been accepted. For A: Question about sam flags.
Scholar 11 months ago, created an answer that has been accepted. For A: Question about sam flags.
Guru 12 months ago, received more than 100 upvotes.
Scholar 13 months ago, created an answer that has been accepted. For A: Velvet-SC installation/compilation issues
Good Answer 16 months ago, created an answer that was upvoted at least 5 times. For A: Question about sam flags.
Scholar 18 months ago, created an answer that has been accepted. For A: Velvet-SC installation/compilation issues
Scholar 18 months ago, created an answer that has been accepted. For A: Velvet-SC installation/compilation issues
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Question about sam flags.
Commentator 18 months ago, created a comment with at least 3 up-votes. For C: SAM file: same reads ID, slightly different sequence
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Question about sam flags.
Good Answer 19 months ago, created an answer that was upvoted at least 5 times. For A: Question about sam flags.
Appreciated 19 months ago, created a post with more than 5 votes. For A: Question about sam flags.
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: Question about sam flags.
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Question about sam flags.
Good Answer 2.6 years ago, created an answer that was upvoted at least 5 times. For A: Question about sam flags.
Scholar 2.7 years ago, created an answer that has been accepted. For A: Velvet-SC installation/compilation issues
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Question about sam flags.
Appreciated 3.0 years ago, created a post with more than 5 votes. For A: Question about sam flags.
Scholar 3.0 years ago, created an answer that has been accepted. For A: Velvet-SC installation/compilation issues
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Error Calling Samtools View On Bwa Sam Output
Scholar 3.4 years ago, created an answer that has been accepted. For A: Velvet-SC installation/compilation issues
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Error Calling Samtools View On Bwa Sam Output

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