Entering edit mode
6.9 years ago
AHW
▴
90
I am trying to use bowtie
tool to align ecoli paired end reads. My files extension is .fq
. The reads look like
@r0/1
TATTCTTCCGCATCCTTCATACTCCTGCCGGTCAG
+
EDCCCBAAAA@@@@?>===<;;9:99987776554
@r1/1
TGATAGATCTCTTTTTTCGCGCCGACATCTACGCC
+
EDCCCBAAAA@@@@?>===<;;9:99987776554
@r2/1
CACGCCCTTTGTAAGTGGACATCACGCCCTGAGCG
+
EDCCCBAAAA@@@@?>===<;;9:99987776554
@r3/1
CGATGCAGATGCGTACCACCTGGACCAGGCCTTTC
+
EDCCCBAAAA@@@@?>===<;;9:99987776554
and I think the reads are in fastq format. But I get the error: on using the following command
bowtie index -1 file1 -2 file2 output
Error: reads file does not look like a FASTQ file
I am not sure what is going wrong.