Hello everyone,
I got a nextseq run that I demultiplexed using bcl2fastq.
Then I used fastq illumina filter and I got this strange result :
According to the website where I've downloaded this software :
Indeed, all my reads (the 4 lanes) have the "N" tag I checked with the following command
Why all my reads have the "N" tag ? According to the bcl2fastq user guide this tag DOES exist with bcl2fastq ! (page 22) So, is there a way to filter reads which are produced with bcl2fastq ? Do I have to update the RTA version ? And finally why fastq_illumina_filter gave me 9% of read passing filter ?
I got a nextseq run that I demultiplexed using bcl2fastq.
Then I used fastq illumina filter and I got this strange result :
fastq_illumina_filter (--keep N) statistics:
Input: 141,900,316 reads
Output: 141,900,316 reads (9%)
Input: 141,900,316 reads
Output: 141,900,316 reads (9%)
This program can filter FASTQ files produced by CASAVA 1.8
grep -A 3 '^@.* [^:]*:Y:[^:]*:'
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