User: John Marshall

gravatar for John Marshall
John Marshall1.2k
Reputation:
1,160
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Location:
Glasgow, Scotland
Twitter:
jomarnz
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an hour ago
Joined:
6 years, 1 month ago
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k********@gmail.com

Posts by John Marshall

<prev • 66 results • page 1 of 7 • next >
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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 4 weeks ago by John Marshall1.2k
3
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1
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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 5 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 5 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 6 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 6 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
... The BAM “run of 0xFF values” is thus so that the offset within the record to the auxiliary data is the same regardless of QUAL data being present or absent. ...
written 6 months ago by John Marshall1.2k
2
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Answer: A: PandaSeq install error: ltld required, install libtool library
... The file it's looking for is `ltdl.h`. A web search for "red hat ltdl.h" shows that this will be supplied by the **libtool-ltdl-devel** package, which is a separate subsidiary of the **libtool** package that provides the `/usr/bin/libtool` that is present. It's possible to install this development ...
written 7 months ago by John Marshall1.2k
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Comment: C: When is the SM tag different for different reads of the same sample?
... The friendlier URL is http://samtools.github.io/hts-specs/SAMtags.pdf — better to point people to that than to an URL containing details like branch names that may change in future. ...
written 8 months ago by John Marshall1.2k
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Comment: C: samtools/tabix with https support?
... README.md is a different file containing different information that is less relevant here. The INSTALL and README files I referred to are in the release tarballs that Alex will have downloaded and also in the Git source repositories. ...
written 9 months ago by John Marshall1.2k
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Answer: A: samtools/tabix with https support?
... Yes. You might look at the documentation in the INSTALL files in htslib and samtools, and also at samtools's README. ...
written 9 months ago by John Marshall1.2k

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?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Question about sam flags.
Scholar 5 months ago, created an answer that has been accepted. For A: Question about sam flags.
Scholar 7 months ago, created an answer that has been accepted. For A: Question about sam flags.
Guru 8 months ago, received more than 100 upvotes.
Scholar 9 months ago, created an answer that has been accepted. For A: Velvet-SC installation/compilation issues
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: Question about sam flags.
Scholar 14 months ago, created an answer that has been accepted. For A: Velvet-SC installation/compilation issues
Scholar 14 months ago, created an answer that has been accepted. For A: Velvet-SC installation/compilation issues
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Question about sam flags.
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: SAM file: same reads ID, slightly different sequence
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Question about sam flags.
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.
Appreciated 23 months ago, created a post with more than 5 votes. For A: Question about sam flags.
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Question about sam flags.
Good Answer 2.3 years ago, created an answer that was upvoted at least 5 times. For A: Question about sam flags.
Scholar 2.4 years ago, created an answer that has been accepted. For A: Velvet-SC installation/compilation issues
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Question about sam flags.
Appreciated 2.7 years ago, created a post with more than 5 votes. 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: Error Calling Samtools View On Bwa Sam Output
Scholar 3.1 years ago, created an answer that has been accepted. For A: Velvet-SC installation/compilation issues
Teacher 3.1 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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