Hellow, Can someone kindly let me know that how to remove a specific read from paired end fastq file using awk or any other command...???
some example data would help. If you know the read by id, then try (seqkit is available here and you can write output to fastq)
$ seqkit grep -r -p <read_id> -v input.fastq
example:
$ seqkit grep -v -rp 'K00193:38:H3MYFBBXX:4:2119:24527:21657/1' hcc1395_normal_rep1_r1.fastq.gz
Thank you so much for kind support. im newbie to NGS and linux and interested to know that Is it possible to remove specific reads using linux commands only rather to use ant toolkit. thank
Assuming that you have fastq gzipped,
$ zgrep "@" input.fastq.gz | grep -v "<readname to be excluded>" | while read line; do zgrep -A 3 $line input.fastq.gz ; done
Please direct the output to a file of your choice
$ zgrep "@" input.fastq.gz | grep -v "<readname to be excluded>" | parallel zgrep -A 3 {} input.fastq.gz
If you have fastq unzipped, try this:
$ sed -n '/@/!d; /< read name>/!p' test.fastq | grep -A 3 -f - test.fastq
(note: if sample read id contains strand information (/1 or /2), make sure that they are escaped. For eg. if read id is K00193:38:H3MYFBBXX:4:2119:24527:21657/1, sed command would be:
$ sed -n '/@/!d; /K00193:38:H3MYFBBXX:4:2119:24527:21657\/1/!p' test.fastq | grep -A 3 -f - test.fastq
thank you so much for kind help.. I will try it and will discuse the output,.. many thanks agauin..
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