Using PRINSEQ lite with zipped paired-end illumina reads
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8.0 years ago
Medhat 9.4k

I have a directory contains 42 paired-end read Illumina they are zipped,

for example;

s245-11kb_1_R1.fq.gz     s245-11kb_1_R2.fq.gz


Is there a way to filter and trim them using prinseq-lite, all in the same time and also zipped?!

from the manual I can see that:

fastq

Input file in FASTQ format that contains the sequence and quality data. Use stdin instead of a file name to read from STDIN (-fasta stdin). This can be useful to process compressed files using Unix pipes

fastq2

For paired-end data only. Input file in FASTQ format that contains the sequence and quality data. The sequence identifiers for two matching paired-end sequences in separate files can be marked by /1 and /2, or _L and _R, or _left and _right, or must have the exact same identifier in both input files. The input sequences must be sorted by their sequence identifiers. Singletons are allowed in the input files.

It did not talk about the zipped version in fastq2 or how to use multiple files

I am using stand alone version

prinseq next-gen-sequencing quality-reads Illumina • 4.0k views
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Can you use process substitution? ./prinseq <your parameters> <(gzip -d -c s245-11kb_1_R2.fq.gz)? This will unzip file on the fly and write it out to stdin.

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That is ok but it is a directory contain 42 file not only the one I write