Hi All,
I have a very naive question. When I use "grep" on one of my fastq files to check the number of reads I get a certain value.
However, When I check the prep_reads.log file after a tophat run I get a different number of reads
40042015 are in the fastq file, but Tophat says the number is 26976249. Is the program not taking all the reads as input?
Please help so I know if I have to run the program again.
Thanks
Abhijit
I have a very naive question. When I use "grep" on one of my fastq files to check the number of reads I get a certain value.
Code:
grep "@" SRR072905.fastq | wc -l 40042015
Code:
more prep_reads.log prep_reads v1.1.4 (1709) --------------------------- 4060 out of 26976249 reads have been filtered out
Please help so I know if I have to run the program again.
Thanks
Abhijit
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