Moderator: John Marshall
John Marshall ♦ 2.0k
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- Glasgow, Scotland
- Twitter:
- jomarnz
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- 6 hours ago
- Joined:
- 8 years, 4 months ago
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Posts by John Marshall
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4
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... 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 22 days ago by
John Marshall ♦ 2.0k
1
vote
1
answer
130
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1
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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 3 months ago by
John Marshall ♦ 2.0k
2
votes
3
answers
260
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3
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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 4 months ago by
John Marshall ♦ 2.0k
3
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1
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186
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1
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... 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 4 months ago by
John Marshall ♦ 2.0k
1
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1
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259
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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 months ago by
John Marshall ♦ 2.0k
0
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1
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264
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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 months ago by
John Marshall ♦ 2.0k
3
votes
1
answer
264
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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 months ago by
John Marshall ♦ 2.0k
1
vote
2
answers
249
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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 6 months ago by
John Marshall ♦ 2.0k
7
votes
1
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213
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1
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... 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 7 months ago by
John Marshall ♦ 2.0k
3
votes
1
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373
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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 8 months ago by
John Marshall ♦ 2.0k
Latest awards to John Marshall
Teacher
22 days ago,
created an answer with at least 3 up-votes.
For A: sam header is not recognized by awk?
Scholar
4 months ago,
created an answer that has been accepted.
For A: Need help interpreting gdb backtrace from a SAMtools segmentation default (or he
Teacher
4 months ago,
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For A: sam header is not recognized by awk?
Scholar
5 months ago,
created an answer that has been accepted.
For A: Need help interpreting gdb backtrace from a SAMtools segmentation default (or he
Teacher
5 months ago,
created an answer with at least 3 up-votes.
For A: sam header is not recognized by awk?
Good Answer
7 months ago,
created an answer that was upvoted at least 5 times.
For A: Question about sam flags.
Scholar
7 months ago,
created an answer that has been accepted.
For A: SAMtools-1.2 sort options documentation
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: sam header is not recognized by awk?
Teacher
8 months ago,
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For A: sam header is not recognized by awk?
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10 months ago,
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For A: SAMtools-1.2 sort options documentation
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11 months ago,
created an answer that was upvoted at least 5 times.
For A: Duplicate @Sq Lines In Sam File Header
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11 months ago,
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For A: Duplicate @Sq Lines In Sam File Header
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11 months ago,
created an answer with at least 3 up-votes.
For A: sam header is not recognized by awk?
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11 months ago,
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For A: SAMtools-1.2 sort options documentation
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13 months ago,
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For A: SAMtools-1.2 sort options documentation
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13 months ago,
created an answer with at least 3 up-votes.
For A: sam header is not recognized by awk?
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19 months ago,
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For A: Tool for random access to indexed BAM files in S3?
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19 months ago,
created a post with more than 5 votes.
For A: Tool for random access to indexed BAM files in S3?
Teacher
19 months ago,
created an answer with at least 3 up-votes.
For A: sam header is not recognized by awk?
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19 months ago,
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For A: SAMtools-1.2 sort options documentation
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For C: SAM file: same reads ID, slightly different sequence
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For A: Tool for random access to indexed BAM files in S3?
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19 months ago,
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For A: sam header is not recognized by awk?
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