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Search: Posts Made By: nora
Forum: Bioinformatics 03-12-2012, 04:24 AM
Replies: 27
Views: 8,575
Posted By nora
Sorry ritzriya, I forgot you need to save the...

Sorry ritzriya, I forgot you need to save the header of your file to a separate file and then concatenate them (e.g. with the cat command) after awk filtering.
Forum: Bioinformatics 03-05-2012, 03:39 AM
Replies: 27
Views: 8,575
Posted By nora
Hi ritzriya, if this is the exact command...

Hi ritzriya,

if this is the exact command you used then awk is missing the input and didn't remove anything... I would use samtools view to pipe the output to the awk command and then write the...
Forum: Bioinformatics 03-05-2012, 03:25 AM
Replies: 27
Views: 8,575
Posted By nora
Sorry, I meant the commands for generating the...

Sorry, I meant the commands for generating the BAM file with the removed operators ;)
Forum: Bioinformatics 03-05-2012, 03:16 AM
Replies: 27
Views: 8,575
Posted By nora
Hi ritzriya, maybe you can post the commands...

Hi ritzriya,

maybe you can post the commands you used for generating the BAM file? Did you remove only the padding operators or others too?

Cheers
Forum: Bioinformatics 01-31-2012, 12:24 AM
Replies: 27
Views: 8,575
Posted By nora
Hi Greg, I'd like to add that, oddly enough,...

Hi Greg,

I'd like to add that, oddly enough, not *every* CIGAR string that is starting with a different operator is causing a problem. If I take, say, the first 200000 reads in my converted BAM...
Forum: Bioinformatics 01-27-2012, 01:52 AM
Replies: 27
Views: 8,575
Posted By nora
Thanks a lot! I just had a look at the CIGAR...

Thanks a lot! I just had a look at the CIGAR strings causing problems, and indeed it seems that everything that doesn't start with the match operator causes the samtools error.

This is less than...
Forum: Bioinformatics 01-27-2012, 12:44 AM
Replies: 27
Views: 8,575
Posted By nora
I'm having the exact same problem (Complete...

I'm having the exact same problem (Complete Genomics data converted to BAM with CGA tools, same error with samtools).

I tried removing the reads with padding operators at the beginning or end of...
Forum: Bioinformatics 09-16-2010, 03:42 AM
Replies: 2
Views: 2,540
Posted By nora
Thanks so much!

Thanks so much!
Forum: Bioinformatics 09-15-2010, 07:19 AM
Replies: 2
Views: 2,540
Posted By nora
BFAST mapping quality scores

Dear all,

Can anybody tell me what the BFAST mapping scores stand for? I know they go from 0-255 but I wonder how they are computed; and do they have anything to do with the probability of a false...
Forum: Bioinformatics 05-12-2010, 09:33 AM
Replies: 3
Views: 5,070
Posted By nora
Thanks for your advice!

Thanks for your advice!
Forum: Bioinformatics 05-11-2010, 06:59 AM
Replies: 3
Views: 5,070
Posted By nora
BWA: specifying SAM/BAM file header fields before read alignment?

Dear all,

I have found the modification of SAM/BAM file headers quite cumbersome and time-consuming, so I wonder if it is planned to include an option into BWA to specify header fields before...
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