User: dariober
dariober • 7.9k
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Posts by dariober
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... I think [pysamstats][1] will do the job here with something like:
pysamstats -f ref.fa --type variation_strand aln.bam > aln.var.txt
[1]: https://github.com/alimanfoo/pysamstats
...
written 1 day ago by
dariober • 7.9k
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... This may be a question in itself but maybe it fits well in this thread...
What's the purpose of the [SRA][1] format? Every question about it seems to be about converting from sra to fastq which makes me wonder whether the sra format was at all necessary.
(Then of course, in hindsight it's easy to ...
written 5 days ago by
dariober • 7.9k
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... I think you should replace `rec.getHeader()` with:
rec.getHeader().getTextHeader() ...
written 9 days ago by
dariober • 7.9k
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... >FASTQ file is expected to start with '@', but found '\n'
If this is true It seems you have an empty line in your fastq. Try to locate it with:
grep -A 10 -B 10 -n '^$' myreads.fastq
This could help finding out what happened ...
written 26 days ago by
dariober • 7.9k
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Comment:
C: tabix for ID column
... Is `join` going to be faster then a sequential scan using e.g. `grep rs1234` or `grep -f rsid.txt`? ...
written 27 days ago by
dariober • 7.9k
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Answer:
A: tabix for ID column
... You could put your table in a sqlite database and index the ID column. Then retrieving records by ID will be very fast. However, this would require working with a sqlite file and associated SQL syntax rather than with the usual unix/R/python tools.
...
written 27 days ago by
dariober • 7.9k
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... Just a couple of things... You should print the sam header as it is, without incrementing the 5th column. I.e. with something like `if($0 ~ "^@") {print $0} else {...}`. Also you should check that incrementing the MAPQ doesn't make it out of bound, i.e. no more than 254 (255 meaning not available). ...
written 27 days ago by
dariober • 7.9k
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Comment:
C: samtools view region
... > it does not matter which end is obtained by the given list of intervals
Exactly, so if the start of an interval (a read) is outside the interval, the OP wants to reject it. The OP wants to keep reads whose start is inside the interval. So if the read has start and end coordinates chr1:5-20 and ...
written 29 days ago by
dariober • 7.9k
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Comment:
C: samtools view region
... It says you can use bam as input, but you can't tell bedtools to output a read if the start is inside a target interval. If a read starts before the interval and ends somewhere inside or after the interval, bedtools will print it. The OP wants to discard such reads instead. Did I get it right? ...
written 29 days ago by
dariober • 7.9k
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174
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Answer:
A: samtools view region
... Would this work, without resorting on additional third party tools?
samtools view aln.bam X:100-1000 | awk -v FS='\t' '$4 >= 100 && $4 <= 1000'
If you want also the bam header:
samtools view -h aln.bam X:100-1000 | awk -v FS='\t' '$1 ~ "^@" || ($4 >= 100 && $4 &l ...
written 29 days ago by
dariober • 7.9k
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