Forum: Bioinformatics
01-24-2012, 03:28 AM
|
|
Replies: 2
Views: 2,559
|
|
Forum: Bioinformatics
01-24-2012, 01:16 AM
|
|
Replies: 2
Views: 2,559
Bowtie2 ( not running with option --sam-rg
Hello,
If I run bowtie2 as below, everything works fine:
bowtie2 --local -x reference.fasta -U in.fastq -S out.sam
But if I use the --sam-rg option i.e.:
bowtie2 --sam-rg 'ID:IL7LANE7'...
|
|
Forum: Bioinformatics
01-10-2012, 03:24 AM
|
|
Replies: 6
Views: 9,189
I had to do:
samtools view -Sb -T...
I had to do:
samtools view -Sb -T reference.fasta out.sam > out.bam
to each split, to get the header...
I don't think that the "samtools reheader" would have worked as you describe it in this...
|
|
Forum: Bioinformatics
12-14-2011, 12:28 PM
|
|
Replies: 5
Views: 3,497
|
|
Forum: Bioinformatics
12-14-2011, 07:13 AM
|
|
Replies: 5
Views: 3,497
|
|
Forum: Bioinformatics
12-14-2011, 06:47 AM
|
|
Replies: 5
Views: 3,497
|
|
Forum: Bioinformatics
06-13-2011, 03:44 AM
|
|
Replies: 3
Views: 2,108
|
|
Forum: Bioinformatics
02-04-2011, 01:35 AM
|
|
Replies: 4
Views: 3,823
The proposed solution with "mpileup -I" has...
The proposed solution with "mpileup -I" has indeed avoided the crash+error, but at the same time it renders samtools to a snp caller only. No indels are called.
I had done an svn checkout of the...
|
|
Forum: Bioinformatics
02-03-2011, 10:12 AM
|
|
Replies: 1
Views: 3,001
454 transcriptome analysis
Hi,
I have a question regarding the 454 transcriptome (cdna) analysis.
Would it be correct to assume that a 454AllContigs.fna in newbler cDNA assembly directory is a non-redundant version of...
|
|
Forum: Bioinformatics
02-03-2011, 09:55 AM
|
|
Replies: 4
Views: 3,823
samtools mpileup unexpected behaviour
Hi,
The command below:
samtools mpileup -ugf 454AllContigs.fasta my.bam | bcftools view -bvcg - > var.raw.bcf
exits with the following error:
[mpileup] 2 samples in 1 input files...
|
|
Forum: Bioinformatics
09-10-2010, 02:38 AM
|
|
Replies: 11
Views: 4,200
|
|
Forum: Bioinformatics
08-03-2010, 02:14 PM
|
|
Replies: 13
Views: 15,605
Hi Zigster,
Thank you very much. It is now...
Hi Zigster,
Thank you very much. It is now clear. Especially the perl example was, as you've pointed out, very enlightening.
A pity that your explanation is not included in the official...
|
|
Forum: Bioinformatics
08-03-2010, 07:22 AM
|
|
Replies: 13
Views: 15,605
BWA manual's -q description too technical
Can someone please explain in normal language what is meant with the option -q in BWA manual and what criteria one should take into consideration when choosing a value for this parameter?
i.e.:...
|
