Question: Chip-seq reads' trimming
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
gravatar for Chirag Nepal
5.7 years ago by
Chirag Nepal2.3k
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
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
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