FASTQ format question

[ashah]

I am having trouble determining the file format of this 'fastq' file... I don't really know anything about the data other than its a small-rna sequence file

The format is

USI-EAS7_2:6:1:724:415:GCT...CCG:hhh...QhG

Does anyone know the name of this format? Or better yet, know a script or something to change it to look like this type of fastq

@HWI-E2_0001:2:1:1115:15158#0/1
GGA...ACT
+HWI-E2_0001:2:1:1115:15158#0/1
aaa...aaa

any input would be greatly appreciated

[drio]

Try the s_*_sequence.txt files from your GERALD output.

[dawe]

I am having trouble determining the file format of this 'fastq' file... I don't really know anything about the data other than its a small-rna sequence file

The format is

USI-EAS7_2:6:1:724:415:GCT...CCG:hhh...QhG

Does anyone know the name of this format? Or better yet, know a script or something to change it to look like this type of fastq

@HWI-E2_0001:2:1:1115:15158#0/1
GGA...ACT
+HWI-E2_0001:2:1:1115:15158#0/1
aaa...aaa

any input would be greatly appreciated

Assuming you have awk installed, you can try this:

awk -F : '{OFS=""; print "@",$1,":",$2,":",$3,":",$4,":",$5,"\n",$6,"\n+\n",$7}'input.txt > output.fastq

HTH

d

[ashah]

Thanks dawe,

I actually did some research and found that it is an older format called SCARF that various programs used to use for alignment purposes. The newest Maq package actually has a scarf2fastq perl script that helped a lot.