Question: fastq quality trimmer
0
gravatar for abhilashreddy495
2.2 years ago by
abhilashreddy4950 wrote:
#fastq_quality_trimmer -v -t 30 -z -i out2.fastq -o out2tt.fastq

this is the code i have run but my ngs data has 150bps after the code run this result is shown 120 bps.

#fastq_quality_trimmer: found empty nucleotide sequence on line 876486

what are the empty nucleotide sequence

rna-seq fastx-tools • 1.1k views
ADD COMMENTlink modified 2.2 years ago by Alex Reynolds29k • written 2.2 years ago by abhilashreddy4950
1

A first approach would be to look at it by eye:

gzcat fastq.gz | sed -n 876486,876487p

Or sed directly, if not compressed.

ADD REPLYlink written 2.2 years ago by ATpoint26k

thank you there is a mistaken in the format

ADD REPLYlink written 2.2 years ago by abhilashreddy4950
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