SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Quality-, adapter- and RRBS-trimming with Trim Galore! fkrueger Bioinformatics 132 04-18-2017 02:04 AM
Adapter trimming figo1019 RNA Sequencing 1 04-07-2014 11:58 AM
Adapter trimming and trimming by quality question alisrpp Bioinformatics 5 04-08-2013 05:55 PM
adapter trimming - help a_mt Bioinformatics 6 11-12-2012 08:36 PM
3' Adapter Trimming caddymob Bioinformatics 0 05-27-2009 01:53 PM

Reply
 
Thread Tools
Old 10-25-2017, 11:51 PM   #281
boulund
Member
 
Location: Sweden

Join Date: Jan 2017
Posts: 16
Default

Hi!

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.
boulund is offline   Reply With Quote
Old 11-20-2017, 10:38 AM   #282
mcmc
Junior Member
 
Location: Midwest, USA

Join Date: Jan 2016
Posts: 8
Default Seal not printing outu file

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

Code:
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?

Thanks,
MC
mcmc is offline   Reply With Quote
Reply

Tags
adapter, bbduk, bbtools, cutadapt, trimmomatic

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:20 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO