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Forum: Bioinformatics 01-15-2016, 02:02 AM
Replies: 347
Views: 185,353
Posted By willd
Dear Brian, indeed there seems to be a...

Dear Brian, indeed there seems to be a "@HISEQ....." line missing in this region of the file, and I found that this has happened in at least one other part of the file as well. I guess I will check...
Forum: Bioinformatics 01-14-2016, 02:08 AM
Replies: 347
Views: 185,353
Posted By willd
Dear Brian, for one fastq file I got the error...

Dear Brian, for one fastq file I got the error output below. FastQC did not show any particular problems with this file. The error refers to a specific read - could there be a problem for BBDuk to...
Forum: Bioinformatics 01-13-2016, 04:11 AM
Replies: 347
Views: 185,353
Posted By willd
Dear Brian - thanks very much! In case it's...

Dear Brian - thanks very much!

In case it's of interest: I tried both 1 pass (contaminant filtering at same time as adapter-trimming) and 2 pass (adapter trimming then contaminant filtering) on...
Forum: Bioinformatics 01-11-2016, 01:39 AM
Replies: 347
Views: 185,353
Posted By willd
Dear Brian, I have many reads from a very...

Dear Brian,

I have many reads from a very specific scRNA contaminant of length 299 bp. Would BBDuk's contaminant filtering be a suitable tool for removing these, and what parameters would you...
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