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Is It Fastq Format

Dear All,

I received the Illumina data in following given format, which neither I can convert to Fastq fit file via any perl script, nor I can utilizes this format of data for subsequent assembling process. Any suggestion will be highly appreciated in this regard.

Asifullah (email redacted)

TAbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbcbbbbbbbbbbbbbbbbbbbbbbbcbbcacbbbbcabb 7vO0qah[aaaaaaAGAGCGCGAGGGAGGAGGAGGAAGAAGAACGCGAGAACGGCGAGGAGGGAGATAGGTTACCGAGAACAATGA TAbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbWabbabbbbbbabbbbbabbbbb_bb 3Ty8qah[aaaaaaGTTGACAATAAGTTCTTTCAAAATTGACTATTTGTCCCTCTGTTAGAGGTGTTCCAGAAATGTCTGCGATCG TAbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbcbbbbbbbbbbbbcbbbbbccbb 5pW8qah[aaaaaaAATGTATTTGCTAATGCCAAAAAGAATCGACCAAAAAAAAAATGACAAAAAGAAAAAAGCAAAATCTGCGAT TAbbbbbbbbbbbbbbbbbbbbbbbbaaabbbbbbbbbbbaaaaabbbbbbbaaaaaaaabbbbbbbbbbbbb `1_eg8qah[aaaaaaTTGATTGAGAAGTGCATTCAGCTGTACATGGACCGTGATGAAACAGTCCGAGCCATAGAAATTCATGCCGCG

fastq illumina next-gen-sequencing
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updated by Neilfws Neilfws • written by Asifullah Khan • Asifullah Khan

3 answers

It certainly is not FASTQ format. I don't know what it is - it almost looks like a binary file. Since you "received" it, I'd contact whoever sent it and get them to clarify.

• 0 views • link
written by Neilfws Neilfws

Is this what the entire file looks like?

Perhaps this is a combination of quality scores and base calls. However, the "quality scores" run short of the sequence. (Except for the last one)

TAbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbcbbbbbbbbbbbbbbbbbbbbbbbcbbcacbbbbcabb
7_vO0qah[aaaa__aaAGAGCGCGAGGGAGGAGGAGGAAGAAGAACGCGAGAACGGCGAGGAGGGAGATAGGTTACCGAGAACAATGA
TAbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbWabbabbbbbbabbbbbabbbbb_bb
3_Ty8qah[aaaa__aaGTTGACAATAAGTTCTTTCAAAATTGACTATTTGTCCCTCTGTTAGAGGTGTTCCAGAAATGTCTGCGATCG
TAbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbcbbbbbbbbbbbbcbbbbbccbb
5_pW8qah[aaaa__aaAATGTATTTGCTAATGCCAAAAAGAATCGACCAAAAAAAAAATGACAAAAAGAAAAAAGCAAAATCTGCGAT
TAbbbbbbbbbbbbbbbbbbbbbbbbaaabbbbbbbbbbbaaaaabbbbbbbaaaaaaaa_bbbbbbbbbbbbb
`1_eg8qah[aaaa__aaTTGATTGAGAAGTGCATTCAGCTGTACATGGACCGTGATGAAACAGTCCGAGCCAT

Very strange...

• 2 views • link
updated by Ram Ram • written by Science_Robot Science_Robot

To have the question answered and brought to a conclusion I will repeat Neil's answer below:

It certainly is not FASTQ format. I don't know what it is - it almost looks like a binary file. Since you "received" it, I'd contact whoever sent it and get them to clarify- neilfws

• 2 views • link
updated by Ram Ram • written by Istvan Albert Istvan Albert

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