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Forum: Bioinformatics 09-05-2011, 12:28 AM
Replies: 7
Views: 11,023
Posted By hlwright
I have changed the read names as suggested and...

I have changed the read names as suggested and re-run picard, but am still not happy that it has worked properly.

I also included an extra command in the command line...
Forum: Bioinformatics 09-01-2011, 11:49 AM
Replies: 7
Views: 11,023
Posted By hlwright
Thank you for the reply, I will try your...

Thank you for the reply, I will try your suggestion of changing the read names.

I have tried samtools rmdup but it removes >90% of my reads (as duplicates). :eek: I was hoping for a 'second...
Forum: Bioinformatics 09-01-2011, 02:14 AM
Replies: 7
Views: 11,023
Posted By hlwright
Picard Mark Duplicates help please

I am tying to use Picard MarkDuplicates to remove my pcr duplicates from a human rna-seq bam file. The run was paired-end but I only have about 30% properly paired (that is another story).

My...
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