Forum: Bioinformatics
09-13-2010, 09:45 AM
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Replies: 20
Views: 18,804
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Forum: Bioinformatics
09-13-2010, 06:33 AM
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Replies: 20
Views: 18,804
Hi Rodney and Nilshomer,
I have a similar...
Hi Rodney and Nilshomer,
I have a similar problem. I do add my reference fasta file after the BAM file but all I see are the Ns. I dont even see the reads that have aligned.
Any suggestions?...
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Forum: Bioinformatics
09-09-2010, 02:40 PM
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Replies: 1
Views: 6,710
SOAP:segmentation fault
Hi All,
I am trying to map solexa PE reads (fastq) from different strains onto reference scaffolds file (fasta) using soap2. The questions I have are:
1. The alignment works but it seems that soap...
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Forum: Bioinformatics
09-09-2010, 06:55 AM
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Replies: 11
Views: 7,626
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Forum: Bioinformatics
09-08-2010, 08:56 AM
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Replies: 1
Views: 2,901
samtools pileup output for SNP detection
Hi All,
I aligned 50 bp solexa reads onto a reference genome using bowtie and now I am using samtools pileup -vcf to call SNPs. This is the output it generates:
scaffold179 29989 T A 30 30 60 1 A B...
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Forum: Bioinformatics
09-07-2010, 07:56 AM
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Replies: 7
Views: 5,245
Hi Peromhc,
Did you find a solution to your...
Hi Peromhc,
Did you find a solution to your problem of SOAP2 not reading the file. In my case it seems to read the forward file just fine but when I try to do PE alignment, SOAP come with error...
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Forum: Bioinformatics
09-06-2010, 09:00 AM
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Replies: 11
Views: 7,626
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Forum: Bioinformatics
09-03-2010, 02:20 PM
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Replies: 5
Views: 3,520
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Forum: Bioinformatics
09-03-2010, 06:44 AM
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Replies: 5
Views: 3,520
Hi Nicobxl,
I am running samtools on a 16 core...
Hi Nicobxl,
I am running samtools on a 16 core 64 bit linux server with 256 GB RAM. Going through the samtools manual, I did not notice any performance related command/options. Please let me know if...
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Forum: Bioinformatics
09-03-2010, 06:23 AM
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Replies: 5
Views: 3,520
Samtools pileup filesize limit
Is there a file size limitation for samtools pileup command? I converted a 82GB sam file (output from bowtie) into a 25 GB compressed bam and then sorted it using samtools. Now when I try running...
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Forum: Bioinformatics
09-02-2010, 01:26 PM
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Replies: 6
Views: 5,266
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Forum: Bioinformatics
08-30-2010, 09:53 AM
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Replies: 6
Views: 5,266
Hi peromhc,
I am getting the same error in...
Hi peromhc,
I am getting the same error in samtools faidx command ([fai_build_core] line length exceeds 65535 in sequence). Looked at all the scaffolds in my fasta file and nothing seems out of...
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Forum: Bioinformatics
08-12-2010, 02:20 PM
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Replies: 1
Views: 2,021
Reference Assembly of solexa PE 50 bp reads
Can anyone suggest a command line to generate reference assembly of 17 million solexa 50 bp reads on reference genome index (index generated from fasta file) that can be used for SNP discovery....
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Forum: Bioinformatics
07-28-2010, 02:40 PM
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Replies: 5
Views: 2,242
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Forum: Bioinformatics
07-28-2010, 07:29 AM
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Replies: 5
Views: 2,242
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Forum: Bioinformatics
07-28-2010, 06:49 AM
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Replies: 5
Views: 2,242
Seqman Leaves most of the reads unaligned
Hi All,
The job at hand it to align 17 million 50 bp illumina reads onto a reference scaffold through Seqman Ngen. The results from the alignment show that approx. 16 million reads remain unaligned...
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