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Old 10-25-2017, 11:51 PM   #281
Location: Sweden

Join Date: Jan 2017
Posts: 16


Is it possible to get the various quality histograms for both before and after e.g. trimming with BBDuk in a single run, or do I need to run BBDuk it twice to produce metrics for before and after trimming?
That is; run once without any trimming, just outputting histograms, and then again to trim and output histograms? Or am I missing something? The histograms output by BBDuk normally show metrics after trimming/contaminant removal, right?

By the way, I might mention that I finally tried to assemble my very large background sample using Tadpole, and then align my primary sample to that to remove 'background/contamination' reads. It produced a fairly poor assembly overall, but at least it ran to completion on the 500GB background sample on my memory constrained machine (64GB). The kmer-based approach was just too memory consuming.

Last edited by boulund; 10-25-2017 at 11:54 PM.
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Old 11-20-2017, 10:38 AM   #282
Location: Midwest, USA

Join Date: Jan 2016
Posts: 14
Default Seal not printing outu file

Hi - I'm running seal to map reads to ref genomes. this is the command I ran:

seal in="${samplename}_nonribo.fq.gz" ref="${all4genomes}" pattern="${samplename}_out_%.fq.gz" outu="${samplename}_unmapped.fq.gz" ambig=all stats="${samplename}_mapstats.txt"
It's outputting the matched reads per reference sequence using the 'pattern', but it's not making the 'outu' file of unmapped reads (and there should be some unmapped reads, according to my stderr output).

Is there another trick to making this file?

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Old 01-19-2018, 12:06 PM   #283
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Location: Florida, USA

Join Date: Mar 2017
Posts: 3

Hi I would like to use bbduk to filter the reads that map to a genome. I have 48 pair samples and want to make sure I understand how to input the file.
My sample are are Pair end and are labeled as F and R (plus _1 and _2).
Should I put them all after in= ? or use in2= for the reverse? Does interleave means that I put each pair together?
eg. in= S1_F_paired_1.fq,S1_R_paired_2.fq,S10_F_paired_1.fq,S10_R_paired_2.fq...

I have them as two separate lines at the moment:


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