Moderator: John Marshall
John Marshall ♦ 1.9k
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- Glasgow, Scotland
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Posts by John Marshall
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2
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3
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205
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... 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 1 day ago by
John Marshall ♦ 1.9k
3
votes
1
answer
92
views
1
answers
... The usage display of `samtools sort` has changed over the years. This one (containing ``, and with `Options: -n` on the same line) indicates that your VM is using the ancient samtools 0.1.19.
This ancient version of `samtools sort` was not capable of reading SAM from standard input (as your pipe fr ...
written 9 days ago by
John Marshall ♦ 1.9k
1
vote
1
answer
117
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1
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... Also look for `913.3` in the fai file:
grep 913.3 ASM584v2.fna.fai
As described in [the documentation](https://www.htslib.org/doc/faidx.5.html), `samtools faidx` considers the **first word** on the `>` lines to be the names of the sequences.
Most aligners do the same thing, and it is surpr ...
written 5 weeks ago by
John Marshall ♦ 1.9k
0
votes
1
answer
149
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1
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Comment:
C: ERROR:SAM to BAM using samtools
... …or which one of those `bowtie` arguments is the input sequence data file anyway… ...
written 5 weeks ago by
John Marshall ♦ 1.9k
3
votes
1
answer
149
views
1
answers
... Your read names `@HISEQ:154:etc` look like SAM headers, so your SAM file is not usable. Read names in SAM files are not allowed to start with `@` characters.
So either your FASTQ file somehow has two `@@` characters at the start of its header lines, or your bowtie mapping pipeline is somehow leavin ...
written 5 weeks ago by
John Marshall ♦ 1.9k
1
vote
2
answers
134
views
2
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... What are the filenames that you are giving to pysam?
If they are cloud URLs and pysam is doing the remote access itself, then this message should already be being suppressed. (At least in the current version of pysam. What version are you using?) The upcoming version of HTSlib takes even more care ...
written 10 weeks ago by
John Marshall ♦ 1.9k
7
votes
1
answer
147
views
1
answers
... If STAR's `nM` was actually identical in function to the standard `NM`, one might ask why on earth they were making life hard for everyone by using a different tag name. But in fact it is not:
> nM : is the number of mismatches per (paired) alignment, not to be confused with NM, which is the num ...
written 11 weeks ago by
John Marshall ♦ 1.9k
3
votes
1
answer
237
views
1
answers
... “Exec format error” indicates that samtools has been unable to recognise the format of your file. Either you ran your bwa command with `nohup` or similar and somehow managed to get some binary characters into it, or there are some other commands you have not shown us that have replaced the file with ...
written 4 months ago by
John Marshall ♦ 1.9k
2
votes
2
answers
250
views
2
answers
... What are the `1112:`, `1113:`, …, `678440:` at the start of the lines of the file you've showed us?
They appear to be some kind of line numbers, and if they're really in the file then of course `samtools` will throw parse errors.
If they're really in the file, you should figure out what in your pi ...
written 5 months ago by
John Marshall ♦ 1.9k
2
votes
4
answers
20k
views
4
answers
... HTSlib has provided a manual page describing this format for a few years now. See `man 5 faidx`, also on the web at [faidx(5) manual page](https://www.htslib.org/doc/faidx.html). ...
written 5 months ago by
John Marshall ♦ 1.9k
Latest awards to John Marshall
Teacher
9 days ago,
created an answer with at least 3 up-votes.
For A: sam header is not recognized by awk?
Scholar
9 days ago,
created an answer that has been accepted.
For A: Need help interpreting gdb backtrace from a SAMtools segmentation default (or he
Scholar
5 weeks ago,
created an answer that has been accepted.
For A: Need help interpreting gdb backtrace from a SAMtools segmentation default (or he
Teacher
5 weeks ago,
created an answer with at least 3 up-votes.
For A: sam header is not recognized by awk?
Good Answer
11 weeks ago,
created an answer that was upvoted at least 5 times.
For A: Question about sam flags.
Scholar
11 weeks ago,
created an answer that has been accepted.
For A: SAMtools-1.2 sort options documentation
Teacher
11 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?
Scholar
6 months ago,
created an answer that has been accepted.
For A: SAMtools-1.2 sort options documentation
Centurion
6 months ago,
created 100 posts.
Appreciated
7 months ago,
created a post with more than 5 votes.
For A: Duplicate @Sq Lines In Sam File Header
Good Answer
7 months ago,
created an answer that was upvoted at least 5 times.
For A: Duplicate @Sq Lines In Sam File Header
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: sam header is not recognized by awk?
Scholar
7 months ago,
created an answer that has been accepted.
For A: SAMtools-1.2 sort options documentation
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: SAMtools-1.2 sort options documentation
Good Answer
15 months ago,
created an answer that was upvoted at least 5 times.
For A: Tool for random access to indexed BAM files in S3?
Appreciated
15 months ago,
created a post with more than 5 votes.
For A: Tool for random access to indexed BAM files in S3?
Teacher
15 months ago,
created an answer with at least 3 up-votes.
For A: sam header is not recognized by awk?
Scholar
15 months ago,
created an answer that has been accepted.
For A: SAMtools-1.2 sort options documentation
Appreciated
15 months ago,
created a post with more than 5 votes.
For A: Tool for random access to indexed BAM files in S3?
Commentator
15 months ago,
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For C: SAM file: same reads ID, slightly different sequence
Teacher
15 months ago,
created an answer with at least 3 up-votes.
For A: sam header is not recognized by awk?
Teacher
15 months ago,
created an answer with at least 3 up-votes.
For A: sam header is not recognized by awk?
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