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spiral01
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GenoMax
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Joel Wallenius
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Recent Replies
Comment: BWA alignment/Samtools; Fail to read the header
by
Pierre Lindenbaum
146k
what i sthat altai5 in front of '@SQ' ?
Comment: BWA alignment/Samtools; Fail to read the header
by
Qboy
•
0
Dear Pierre,
Here is the answer to your questions (Iguess it works):
altai5@SQ SN:NC_036879.1 LN:224244399
@SQ SN:NC_…
Comment: Supplementary alignments in BAM-file
by
cmdcolin
★
2.2k
for what it's worth, "supplementary alignments" can be quite interesting. they often indicate things like SVs
Comment: Filtered reads from assembly and raw reads?
by
GenoMax
117k
In that case use an aligner of your choice and extract reads that map: https://www.biostars.org/p/56246/#56251
Be sure to get primary alig…
Comment: Filtered reads from assembly and raw reads?
by
el97004
▴
50
Yeah I was just trying to find the set of reads that were used to make up the final assembly. Some of those raw reads will definitely not a…
Comment: Filtered reads from assembly and raw reads?
by
GenoMax
117k
Not sure then what your question is. What format is your query data in? That must already be in fastq format? Are you simply looking to ext…
Answer: resolving specific clusters from data (spectral clustering)
by
Mensur Dlakic
★
20k
I think Gaussian mixture models will work well on this type of scatter, though you will likely end up with more than two clusters. If you p…
Comment: Filtered reads from assembly and raw reads?
by
el97004
▴
50
Thanks @genomax ! Once aligned and obtained bam file could I not then just convert that to fastq?
Comment: What would the items look like if we put them on a length scale?
by
Mensur Dlakic
★
20k
What you are suggesting is a trivial conversion, so your AU (astronomic unit) can be any other AU (arbitrary unit). It may work well for ev…
Comment: txt file process in linux
by
ohu20a
▴
10
This should work:
awk '$8 > 25 && $7 < 0.01' file.txt
Answer: txt file process in linux
by
cpad0112
21k
Assuming that file is tab de-limited and first column is chr, try this:
$ awk 'NR==1;$5<0.01 && $7>25' input.txt
Comment: The STAR program does not work after the mapping
by
pavelasquezv
▴
20
Hi GenoMax. Many thanks for your help. Now it is working, I think the problem was the insufficient memory. Many thanks my friend!
Comment: The STAR program does not work after the mapping
by
pavelasquezv
▴
20
I am using qsub Pierre. But now it is working, I think the problem was the insufficient memory. Many thanks my friend!
Answer: Supplementary alignments in BAM-file
by
Carlo Yague
8.1k
In one step, you could remove every alignments with a mapping quality of 0. With most aligners, this corresponds to the reads for which the…
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