Forum: Bioinformatics
05-31-2012, 04:46 PM
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Replies: 4
Views: 1,713
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Forum: Bioinformatics
05-31-2012, 03:37 PM
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Replies: 4
Views: 1,713
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Forum: Bioinformatics
05-31-2012, 02:36 PM
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Replies: 4
Views: 1,713
BAM Header minor edit
Hi,
I have around 20 BAM files and each of them have proper bam header including RG ID, Sample, Library, Platform unit, Description and Platform. I was reading the GATK manual and just realized...
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Forum: Bioinformatics
05-21-2012, 08:39 PM
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Replies: 3
Views: 2,833
This is a bug in BWA. If you use -q it puts the...
This is a bug in BWA. If you use -q it puts the trimmed nucleotide read in the output SAM file but the quality sequence is not trimmed at all and thus there is a difference in the length of the read...
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Forum: Bioinformatics
05-17-2012, 11:15 AM
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Replies: 0
Views: 1,339
readgroup id, sample, library confusion
We recently sequenced a specific mouse strain. The sequencing data was generated on the 5500 XL platform from the same mate-pair library from a single male mouse liver. We had our sequencing done on...
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Forum: Bioinformatics
05-11-2012, 02:59 PM
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Replies: 2
Views: 2,211
BWA -n option
I have been trying to use BWA to align my solid reads. In the manual it has been mentioned that you can use the -n option to limit the number of mismatches allowed between reference genome and the...
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Forum: Bioinformatics
04-27-2012, 12:22 PM
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Replies: 2
Views: 3,413
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Forum: Bioinformatics
04-26-2012, 08:53 PM
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Replies: 2
Views: 3,413
Hey I figured it out myself:
The following...
Hey I figured it out myself:
The following commands works:
samtools view -b -f 67,131,179,115 old.bam > new.bam
I am sorry for not giving this enough try before posting. I will not delete the...
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Forum: Bioinformatics
04-26-2012, 08:38 PM
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Replies: 2
Views: 3,413
samtools view
Hi,
I am using samtools view -f option to output mate-pair reads that are properly placed in pair in the bam file.
My command is as follows: (67,131- first read, second read and 115,179 first ,...
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Forum: Bioinformatics
04-26-2012, 03:58 PM
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Replies: 3
Views: 1,331
I have similar questions in this post: ...
I have similar questions in this post:
http://seqanswers.com/forums/showthread.php?t=19537
I used the following tool to figure it out but I am not sure if all of my steps are right....
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Forum: Bioinformatics
04-26-2012, 03:54 PM
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Replies: 5
Views: 3,030
Hi,
If you use BWA can you comment on my...
Hi,
If you use BWA can you comment on my questions. I mean "Am i using the correct flags" because when I used these flags my BAM file reduced from 18 gb to 4 gb. I dont care about the unmapped or...
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Forum: Bioinformatics
04-26-2012, 10:50 AM
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Replies: 5
Views: 3,030
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Forum: Bioinformatics
04-25-2012, 05:22 PM
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Replies: 5
Views: 3,030
BWA and SAMtools
Hello Everyone,
I used BWA to align SOLiD mate pair reads (60,60) with parameters -n 8(total mismatch) -l 25 (seed) and -k 2 (mismatch in seed). I am getting a good mapping rate of around 65%. I...
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Forum: Bioinformatics
04-25-2012, 05:06 PM
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Replies: 14
Views: 17,959
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Forum: Bioinformatics
02-23-2012, 02:46 PM
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Replies: 1
Views: 1,768
Copied from MAQ Documentation at...
Copied from MAQ Documentation at http://maq.sourceforge.net/qual.shtml
What is Mapping Quality?
In a probabilistic view, each read alignment is an estimate of the true alignment and is...
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Forum: Bioinformatics
02-23-2012, 02:36 PM
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Replies: 1
Views: 3,818
Lifescope comes with all the tertiary analysis...
Lifescope comes with all the tertiary analysis (SNP calling, indel, annotation) modules. They have a very nice mapping analysis. I was able to map ~75-85% of total reads to ref genome at mapping...
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Forum: Genomic Resequencing
11-18-2011, 08:46 AM
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Replies: 0
Views: 1,651
some basic queries (mapping)
Hi everyone,
I am newbie to sequencing analysis. I would be thankful if someone can answer these questions:-
1) What are uncallable bases in reads? Are these "N" thing in some reads. Because...
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Forum: Bioinformatics
10-30-2011, 10:31 PM
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Replies: 0
Views: 1,958
problem with running MAQ
I downloaded the MAQ and installed it as instructed in the manual. I moved the binary files to /home/user/bin directory and then I could run the maq commands from anywhere. i already converted...
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