Question: Is It Fastq Format
0
gravatar for Asifullah Khan
8.7 years ago by
Asifullah Khan10 wrote:

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 reagrd.


Asifullah (asifullah111@gmail.com)

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

ADD COMMENTlink modified 8.7 years ago by Science_Robot1.1k • written 8.7 years ago by Asifullah Khan10
2

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.

ADD REPLYlink written 8.7 years ago by Neilfws48k
1
gravatar for Science_Robot
8.7 years ago by
Science_Robot1.1k
Gainesville, FL
Science_Robot1.1k wrote:

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...

ADD COMMENTlink written 8.7 years ago by Science_Robot1.1k
0
gravatar for Istvan Albert
8.7 years ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

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

ADD COMMENTlink written 8.7 years ago by Istvan Albert ♦♦ 80k
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