Question: Chip-seq reads' trimming
0
gravatar for marina-orlova
5.7 years ago by
Russian Federation
marina-orlova80 wrote:

Hi all

I have chip-seq reads of bad quality (dm3) - 29,772,199  reads:

 

Tried to trim it with fastq_quality_filter (command line fastq_quality_filter -q 20 -p 100 -i infile.fastq -o outfile.fastq) and got only 410,775 reads:

Is that OK? Otherwise, what should I do to these data? I suppose I should't just push it to bowtie for alignment..

fastqc chip-seq • 3.0k views
ADD COMMENTlink modified 5.1 years ago by Biostar ♦♦ 20 • written 5.7 years ago by marina-orlova80
2
gravatar for Chirag Nepal
5.7 years ago by
Chirag Nepal2.3k
Copenhagen
Chirag Nepal2.3k wrote:

From fig it looks the quality of your sequence is not good. Currently u are throwing out most of your data by trimming. 410775 is too little reads to push to bowtie.

First check if you have primers/adapters attached to beginning/end of sequence. If so, remove them. Look at over-represented sequence, take few of those, blat them to genome individually and see what portion of the sequence maps and what doesn't. That should give you idea about primer/adapter sequence.

Or trim the last 5 or 10 nucleotide, and analyze how mapping differs ? compare with different parameters of trimming. You need to play a bit with your data.

ADD COMMENTlink written 5.7 years ago by Chirag Nepal2.3k
1
gravatar for Brian Bushnell
5.7 years ago by
Walnut Creek, USA
Brian Bushnell17k wrote:

Bowtie is not very tolerant of low-quality reads.  If you want to use this data, I'd suggest aligning with BBMap, and using the raw untrimmed reads.

ADD COMMENTlink written 5.7 years ago by Brian Bushnell17k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1663 users visited in the last hour