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Search: Posts Made By: Sylphide
Forum: Bioinformatics 06-22-2011, 04:30 AM
Replies: 4
Views: 1,785
Posted By Sylphide
The author Bernhard Haubold created a script to...

The author Bernhard Haubold created a script to go from SAMTOOLS pileup to number of A,T,C,G available on asking.

Thanks for your help mgogol anyway :)
Forum: Bioinformatics 06-21-2011, 05:11 AM
Replies: 4
Views: 1,785
Posted By Sylphide
From BAM/SAM to number of A,C,G,T at each location

Hi,
I would like to obtain the number of A,C,G and T at each position of each contig from a SAM/BAM file.

This is tu run the program mlRho from Bernhard Haubold, Peter Pfaffelhuber and Michael...
Forum: Bioinformatics 05-30-2011, 12:06 PM
Replies: 2
Views: 2,569
Posted By Sylphide
SAM/BAM how to retrieve all mapped reads ?

Hello,
I obtained a BAM file from BWA and would like to keep only mapped reads. Samtools view -q 1 removes reads with mapQ 0 and I would like to conserve them.
Does anyone have a solution ?
Many...
Forum: Bioinformatics 04-15-2011, 01:12 PM
Replies: 3
Views: 2,630
Posted By Sylphide
Indeed they have the same read number. Many...

Indeed they have the same read number.
Many thanks for your help !
Forum: Bioinformatics 04-15-2011, 12:56 AM
Replies: 3
Views: 2,630
Posted By Sylphide
Samtools sort output smaller than input

Hello,
I have a problem with samtools sort : my output files are smaller than my input files when they should be identical since only the lines order is changed !
Does anyone know this problem and...
Forum: Bioinformatics 04-06-2011, 08:53 AM
Replies: 4
Views: 2,036
Posted By Sylphide
I know I had some reads that were over-hanging...

I know I had some reads that were over-hanging from the end of the contigs (when mapping RNA seq onto CDS sequences) and it worked fine with BWA.
Forum: Bioinformatics 03-31-2011, 06:42 AM
Replies: 6
Views: 4,565
Posted By Sylphide
I would also like to obtain "alignments" from...

I would also like to obtain "alignments" from SAM/BAM. Since the samtools tview allows to view the alignment it should be possible to obtain these "alignments" in text format, no ?
Forum: Bioinformatics 03-02-2011, 04:19 AM
Replies: 6
Views: 17,909
Posted By Sylphide
I think I found the answers to my questions, I...

I think I found the answers to my questions, I put it here in case it needs corrections or in case it is useful to someone else:

The ID tag in the read group @RG refers to a unique combination of...
Forum: Bioinformatics 03-02-2011, 12:41 AM
Replies: 6
Views: 17,909
Posted By Sylphide
GATK sample/library/lane meaning in BAM read group @RG

Hello
I got puzzled by GATK way of explaining sample/library/lane to detect SNP.
It seems to me that their "sample" is equivalent to an individual. However after reading the SAM Format...
Forum: Illumina/Solexa 02-27-2011, 11:54 PM
Replies: 6
Views: 12,735
Posted By Sylphide
hello I'm also a beginner but I'll try to help....

hello
I'm also a beginner but I'll try to help.
You can use the conversion table I wrote to convert ASCII to numeric if you want to program it yourself. There must be some tool to make the...
Forum: Illumina/Solexa 02-25-2011, 01:54 AM
Replies: 6
Views: 12,735
Posted By Sylphide
I looked for the meaning of illumina quality...

I looked for the meaning of illumina quality scores and couldn't find any direct translation so here it is (in case it is of any use to someone else)

Illumina quality score dictionary :
...
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