Galaxy tool to filter low mapping quality reads?

kwoweiho · 10-01-2012, 02:31 PM

Does anybody know if there is a way to remove low quality reads on Galaxy? it could be easily done using command line based bamtools and all I have to do is specify the map quality. Is there an equivalent version on galaxy? Or is there a published workflow that does it for you? Thanks.

huyvuong · 10-02-2012, 08:46 AM

there is a tool called filter FASTQ (Filter FASTQ reads by quality score and length) under GENERIC FASTQ MANIPULATION

geneart · 10-02-2012, 09:11 AM

Hello,
trying to use galaxy to perform NGS analysis.
I have created a history that contains my datasets. Now when I go down to pull the filterQC application I dont see my datasets in the "library to filter". How do I pull my datasets into the stream?
Tutorial shows how to get data from UCSC and also if I have a work flow created then I can do it, but without a workflow , if I have to just use one tool to do the job how do I get my datasets to show up for an operation?
Thanks for ur time

geneart

mmammel · 08-08-2013, 06:56 AM

Before using Filter FastQ you must use the FASTQ Groomer.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
how to filter low quality reads ?	StephaniePi83	Bioinformatics	14	11-28-2012 07:26 AM
remove illumina low quality reads	StephaniePi83	Bioinformatics	1	04-12-2012 04:12 AM
Using Tophat with low quality Illumina Reads	sphil	Bioinformatics	5	08-02-2011 08:28 AM
Mapping 454 reads using Galaxy online.	Alex Clop	Bioinformatics	1	08-12-2010 06:13 AM
filter high quality solexa reads	strob	Bioinformatics	1	12-08-2009 06:19 AM

10-01-2012, 02:31 PM	#1
kwoweiho Junior Member Location: Iowa Join Date: Oct 2012 Posts: 2	Galaxy tool to filter low mapping quality reads? Does anybody know if there is a way to remove low quality reads on Galaxy? it could be easily done using command line based bamtools and all I have to do is specify the map quality. Is there an equivalent version on galaxy? Or is there a published workflow that does it for you? Thanks.

10-02-2012, 09:11 AM	#3
geneart Member Location: DC area Join Date: Sep 2011 Posts: 42	Galaxy filter quality help Hello, trying to use galaxy to perform NGS analysis. I have created a history that contains my datasets. Now when I go down to pull the filterQC application I dont see my datasets in the "library to filter". How do I pull my datasets into the stream? Tutorial shows how to get data from UCSC and also if I have a work flow created then I can do it, but without a workflow , if I have to just use one tool to do the job how do I get my datasets to show up for an operation? Thanks for ur time geneart

08-08-2013, 06:56 AM	#4
mmammel Junior Member Location: MD Join Date: Aug 2013 Posts: 1	filterQC Before using Filter FastQ you must use the FASTQ Groomer.

10-02-2012, 08:46 AM	#2
huyvuong Member Location: michigan Join Date: Oct 2010 Posts: 10	there is a tool called filter FASTQ (Filter FASTQ reads by quality score and length) under GENERIC FASTQ MANIPULATION