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Forum: Bioinformatics 10-08-2010, 12:26 AM
Replies: 11
Views: 5,829
Posted By cur
how do you make refFlat_RefSeq.gff for mm9

Can somebody tell me where you get the refFlat_RefSeq.gff for mm9? I have found gff3 files for each chromosome (reference assembly, MGSCv37, of mouse build 37.1, in GFF3 format). Do these correspond...
Forum: Illumina/Solexa 04-21-2010, 12:22 AM
Replies: 145
Views: 295,463
Posted By cur
Hi greigite Thanks for the reply- in this case...

Hi greigite
Thanks for the reply- in this case the answer was actually simple in the end- the sequencing service had not sent us the right data. Once we got the right data there was no problem with...
Forum: Illumina/Solexa 03-24-2010, 03:31 AM
Replies: 145
Views: 295,463
Posted By cur
solexa adapter sequences for paired end data

I wonder if somebody can help me here....I have got some solexa data (paired end reads) and want to map these to the genome with bwa/maq...However when I did this only 20% of sequences mapped so...
Forum: Bioinformatics 03-16-2010, 03:00 AM
Replies: 5
Views: 2,687
Posted By cur
tophat installation on ubuntu 9.10 64 bit

Thanks, I also had the problem and thanks to your post got the problem solved.
I Installed gcc-multilib and ran:
./configure CFLAGS="-m64" CXXFLAGS="-m64"
Forum: Bioinformatics 03-04-2010, 04:17 AM
Replies: 11
Views: 10,767
Posted By cur
identification of indels with samtools interpretation of SNP quality

I am trying to identify indels and am having trouble understanding the values in column 5 and 6 of my pileup output (see example of lines in final_aln_ivcf.pileup). As I understand column 5 in...
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