ch4rr0
commented
5 years ago You specified -U but did not provide the required unpaired read file(s). This will cause bowtie2 to error out as your bowtie2_map_001.log file will indicate.
The error message you see is samtools view usage output indicating that the bowtie2 command failed.
Hope this helps.
Edited mistake in response
Hi everyone, I am beginner in Linux and I am trying to do mapping step to identify circRNA in my RNAseq libraries. Here what I have done for it: bowtie2-build Gmax_275_v2.0.fa Gmax_indexed _bowtie2 -p16 --very-sensitive --score-min=C,-15,0 --mm -x /media/......../Gmax_indexed -q -U -1 001FNT1s1_pe -2 001FNT1S2_pe 2> bowtie2_map_001.log | samtools view -hbuS - | samtools sort - test_vs_Celegans But it is not happening with the comment (at the end):
""--reference FILE Reference sequence FASTA FILE [null]""
It would be great if you could help me out with it. Any comments would be appropriated.
Best, Essi