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Forum: Bioinformatics 01-24-2012, 03:28 AM
Replies: 2
Views: 2,559
Posted By CHRYSES
oh thanks a lot! I thought that gods were playing...

oh thanks a lot! I thought that gods were playing tricks on me. Apparently a known issue.

best regards
Forum: Bioinformatics 01-24-2012, 01:16 AM
Replies: 2
Views: 2,559
Posted By CHRYSES
Unhappy 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
Posted By CHRYSES
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
Posted By CHRYSES
Yes, but how can I run a pileup on a single...

Yes, but how can I run a pileup on a single position with 500 million X coverage ? I think i will need to do this read by read...
Forum: Bioinformatics 12-14-2011, 07:13 AM
Replies: 5
Views: 3,497
Posted By CHRYSES
Yeah, I tried to get into that, but I am not good...

Yeah, I tried to get into that, but I am not good at "C" language, I could not follow it. I hope someone else has created/thought of something...

I could go directly into text format (i.e. SAM)...
Forum: Bioinformatics 12-14-2011, 06:47 AM
Replies: 5
Views: 3,497
Posted By CHRYSES
Fastest way to extract differing positions from each alignment in a BAM file

Hi,

What would be the fastest way (I have to do this hundreds of millions times) to extract for each aligned read in a BAM file:
1) The positions where the read bases differ from a reference...
Forum: Bioinformatics 06-13-2011, 03:44 AM
Replies: 3
Views: 2,108
Posted By CHRYSES
a bioinformatics IRC channel for live discussions

Hi,

I would like to propose an IRC channel called "#seqanswers" on irc.freenode.net

That might be handy for fast communication about sequencing related bioinformatics issues.


Best regards
Forum: Bioinformatics 02-04-2011, 01:35 AM
Replies: 4
Views: 3,823
Posted By CHRYSES
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
Posted By CHRYSES
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
Posted By CHRYSES
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
Posted By CHRYSES
I guess you meant: Different "isotigs" within the...

I guess you meant: Different "isotigs" within the same isogroup represent (...)
Forum: Bioinformatics 08-03-2010, 02:14 PM
Replies: 13
Views: 15,605
Posted By CHRYSES
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
Posted By CHRYSES
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.:...
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