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Forum: Bioinformatics 09-13-2010, 09:45 AM
Replies: 20
Views: 18,511
Posted By Mansequencer
Here is the command: samtools tview...

Here is the command:
samtools tview file.sort.bam reference.folded.fas
Forum: Bioinformatics 09-13-2010, 06:33 AM
Replies: 20
Views: 18,511
Posted By Mansequencer
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?...
Forum: Bioinformatics 09-09-2010, 02:40 PM
Replies: 1
Views: 6,617
Posted By Mansequencer
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...
Forum: Bioinformatics 09-09-2010, 06:55 AM
Replies: 11
Views: 7,491
Posted By Mansequencer
Hi Rahul, You were right. I had to rearrange...

Hi Rahul,
You were right. I had to rearrange the command line with the same options that I was using before and it worked.
Thanks.
Forum: Bioinformatics 09-08-2010, 08:56 AM
Replies: 1
Views: 2,867
Posted By Mansequencer
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...
Forum: Bioinformatics 09-07-2010, 07:56 AM
Replies: 7
Views: 5,142
Posted By Mansequencer
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...
Forum: Bioinformatics 09-06-2010, 09:00 AM
Replies: 11
Views: 7,491
Posted By Mansequencer
Hi Rahul, I am having the same issue. How did...

Hi Rahul,
I am having the same issue. How did you resolve the problem?
Thanks so much for your help.
Forum: Bioinformatics 09-03-2010, 02:20 PM
Replies: 5
Views: 3,465
Posted By Mansequencer
Hi Ih3, I am using this command to generate a...

Hi Ih3,
I am using this command to generate a txt file.
samtools pileup -vcf filename.fas filename_sorted.bam > rawsnp.txt

I ran samtools on a 1.7 GB file under 32 bit linux system and it...
Forum: Bioinformatics 09-03-2010, 06:44 AM
Replies: 5
Views: 3,465
Posted By Mansequencer
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...
Forum: Bioinformatics 09-03-2010, 06:23 AM
Replies: 5
Views: 3,465
Posted By Mansequencer
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...
Forum: Bioinformatics 09-02-2010, 01:26 PM
Replies: 6
Views: 5,164
Posted By Mansequencer
Hi Brentp, Thanks for your advice. It worked.

Hi Brentp,
Thanks for your advice. It worked.
Forum: Bioinformatics 08-30-2010, 09:53 AM
Replies: 6
Views: 5,164
Posted By Mansequencer
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...
Forum: Bioinformatics 08-12-2010, 02:20 PM
Replies: 1
Views: 1,996
Posted By Mansequencer
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....
Forum: Bioinformatics 07-28-2010, 02:40 PM
Replies: 5
Views: 2,204
Posted By Mansequencer
Sure. I will give it a shot. Thanks,

Sure. I will give it a shot.
Thanks,
Forum: Bioinformatics 07-28-2010, 07:29 AM
Replies: 5
Views: 2,204
Posted By Mansequencer
Hi nickloman, Thanks for your response. Yes, I...

Hi nickloman,
Thanks for your response. Yes, I was surprised too but the Newbler analysis was done by someone else. It can however complete the job but accuracy and quality is compromised if...
Forum: Bioinformatics 07-28-2010, 06:49 AM
Replies: 5
Views: 2,204
Posted By Mansequencer
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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