Off topic:Error: reads file does not look like a FASTQ file
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Entering edit mode
8.5 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.

software error alignment • 7.3k views
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