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Forum: Bioinformatics 07-12-2012, 10:34 AM
Replies: 2
Views: 1,320
Posted By prbndr
wig file

hi all,

i'm trying to create a wig file in the following format:

track format=wiggle_0
variableStep chrom=2-micron span=1
1340 1
1341 1

where the left column represents a read start...
Forum: Bioinformatics 03-13-2012, 06:13 PM
Replies: 5
Views: 3,281
Posted By prbndr
cufflinks rna-seq coverage

i'm a little confused as to why cufflinks didn't output a coverage estimate in the gene level tracking file. does anyone know what the reason is for this, and how i can derive an estimate of gene...
Forum: Bioinformatics 09-20-2011, 11:43 AM
Replies: 2
Views: 2,045
Posted By prbndr
but they seem to filter variants. how do i...

but they seem to filter variants. how do i completely turn the filter off and output every single variant present in the sam file?
Forum: Bioinformatics 09-20-2011, 11:31 AM
Replies: 2
Views: 2,045
Posted By prbndr
find all snps/indels

is there a good way to find all the snps and indels (or just deletions in the read) from a sam file? has anyone written an MD tag parser that can do this? i tried a workaround by using the samtools...
Forum: Bioinformatics 09-12-2011, 01:36 PM
Replies: 1
Views: 1,504
Posted By prbndr
library mutation profile

are there any tools that can give me a profile of mutations in my library of mapped sequences reads (using BWA)? i'm specifically interested in obtaining the overall percentage of (A->T, A->G, A->C,...
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