User: John Marshall
John Marshall • 1.2k
- Reputation:
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- Location:
- Glasgow, Scotland
- Twitter:
- jomarnz
- Last seen:
- 42 minutes ago
- Joined:
- 6 years, 5 months ago
- Email:
- k********@gmail.com
Posts by John Marshall
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... 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 Marshall • 1.2k
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... You may have installed samtools 1.3 (which is also somewhat out of date at this point), but if it is printing out "[samopen] SAM header is present" then you are actually using samtools 0.1.18 or thereabouts.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 Marshall • 1.2k
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... 1. You are using a prehistoric version of samtools. 2. Did you consider looking at line 31099973? ...
written 3 months ago by
John Marshall • 1.2k
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... 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 Marshall • 1.2k
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... 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 Marshall • 1.2k
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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 Marshall • 1.2k
3
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... 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 Marshall • 1.2k
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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 Marshall • 1.2k
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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 Marshall • 1.2k
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... 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 Marshall • 1.2k
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?
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
Commentator
18 months ago,
created a comment with at least 3 up-votes.
For C: SAM file: same reads ID, slightly different sequence
Good Answer
19 months ago,
created an answer that was upvoted at least 5 times.
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
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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