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Search: Posts Made By: dreesbl
Forum: Bioinformatics 08-17-2011, 02:27 PM
Replies: 17
Views: 13,145
Posted By dreesbl
@ TuA Check the frequency for the SNPs that...

@ TuA

Check the frequency for the SNPs that were found with samtools. One of the options in the mpileup command is:

-p FLOAT A site is considered to be a variant if P(ref|D)<FLOAT [0.5]
...
Forum: Bioinformatics 08-17-2011, 02:03 PM
Replies: 5
Views: 1,273
Posted By dreesbl
@bogdan If you're interested, Spiral...

@bogdan

If you're interested, Spiral Genetics is launching a remote NGS analysis software pipeline that includes a fast-running gapped aligner that is a distributed adaptation of BWA's...
Forum: Bioinformatics 08-17-2011, 01:59 PM
Replies: 2
Views: 1,222
Posted By dreesbl
@dingxaiofan1 Can you explain exactly what...

@dingxaiofan1

Can you explain exactly what you mean when you say "variations from one NGS sample"? Do you mean between that sample and a reference sequence or the between the two haplotypes in...
Forum: Bioinformatics 08-17-2011, 01:33 PM
Replies: 2
Views: 1,057
Posted By dreesbl
@vebaev As you found out, option -a is...

@vebaev

As you found out, option -a is usually trouble! To answer your question, -m 200 means that NO alignments are reported for a read that has 200+ hits. For a read with 1, 2, or 199...
Forum: Bioinformatics 08-17-2011, 12:55 PM
Replies: 4
Views: 4,495
Posted By dreesbl
@ efoss, oghabian, ramouz87 I don't think...

@ efoss, oghabian, ramouz87

I don't think there's any reasonable way to get from one to the other. The alignments you got by treating the reads as singles are not the same as what you'll get if...
Forum: Bioinformatics 08-17-2011, 12:11 PM
Replies: 12
Views: 16,638
Posted By dreesbl
If you're sequencing an equal number of base...

If you're sequencing an equal number of base pairs, I vote for paired end reads. I agree with dcfactor that there won't be much difference between estimates from 50 bp and 100 bp read data if you're...
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