User: Swbarnes2
Swbarnes2 • 1.5k
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Posts by Swbarnes2
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... It doesn't think you have a .bam file. That's a bigger problem than the lack of sorting. ...
written 8.5 years ago by
Swbarnes2 • 1.5k
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... bwa will also do that if you screwed up your command line, and mistyped the name of an input file in a previous step. If you mistyped the name of your fastq in the aln step, I think you still make a .sai file, and sampe will do its best on what it has. So that's a quick thing you can double-check. ...
written 8.5 years ago by
Swbarnes2 • 1.5k
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... I've got many 96-well plates of samples (a library of vectors with various insert sequences, one per well), and they know that some of the wells are cross-contaminated. They are hoping to be able to distingush which wells have < 1% contamination. They have sanger end reads of each wells, coveri ...
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... They might have trimmed out more low-quality reads or repetative reads than you did. ...
written 8.5 years ago by
Swbarnes2 • 1.5k
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... What's so onerous about running samtools view 3 times to split up the .bam into those three groups?
samtools view -bf 64 mixed.bam > read1.bam
samtools view -bf 128 mixed.bam > read2.bam
samtools view -bF 1 mixed.bam > SE.bam
Then run bam2fastq on each of those files.
...
written 8.5 years ago by
Swbarnes2 • 1.5k
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... You could use samtools view to filter the .bam into three files; reads that are read 1, reads that are read 2, and reads from SE experiments. Picard can sort each .bam by read name, before you convert them to fastq. ...
written 8.5 years ago by
Swbarnes2 • 1.5k
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Answer:
A: Sam Tools Pileup Format
... Instead of running a separate program to convert fastq to fasta, vcfutils.pl is easy enough to alter. It's a perl script, so it's a flat text file. Basically, you want the last few lines of vcf2fq to look like this:
print "\>$chr\n"; &v2q_print_str($seq);
# print "+\n"; &v2q_print_st ...
written 8.5 years ago by
Swbarnes2 • 1.5k
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Comment:
C: Markduplicates Error
... Look at a little of the orignal .sam file with your eyeballs. What flags do you see? Is your pipeline possibly changing those flags? ...
written 8.5 years ago by
Swbarnes2 • 1.5k
1
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2
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Answer:
A: Markduplicates Error
... It looks like the software that made your .bam made the flags wrong. It looks like Picard is complainnig that your .bam entries have the 1 flagged, but not 64 or 128.
But as long as your read names are identical between the two reads, Picard might still be able to figure out that they are paired, a ...
written 8.5 years ago by
Swbarnes2 • 1.5k
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... If you want to count across the whole .bam, use samtools flagstat
samtools flagstat -cf 16 -F 4
will count how many mapped reads run in the reverse direction.
samtools flagstat -cF 20
will count how many mapped reads run in the forward direction.
The pileup will work too, periods means forward di ...
written 8.5 years ago by
Swbarnes2 • 1.5k
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