Converting Solexa eland to Solexa fastq

Question

[ChIP]

Hi,

I have a solexa eland file:

SOLEXAWS1       0       5       1       2013    985     0       1       NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN     BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB     QC                                                                                  N
SOLEXAWS1       0       5       1       4049    987     0       1       NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN     BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB     QC                                                                                  N
SOLEXAWS1       0       5       1       4263    988     0       1       NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN     BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB     QC                                                                                  N
SOLEXAWS1       0       5       1       4452    988     0       1       NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN     BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB     QC                                                                                  N
SOLEXAWS1       0       5       1       6118    985     0       1       NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN     BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB     QC                                                                                  N
SOLEXAWS1       0       5       1       7538    983     0       1       NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN     BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB     QC                                                                                  N
SOLEXAWS1       0       5       1       8405    987     0       1       NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN     BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB     QC                                                                                  N
SOLEXAWS1       0       5       1       8645    983     0       1       NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN     BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB     QC                                                                                  N
SOLEXAWS1       0       5       1       8838    987     0       1       NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN     BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB     QC                                                                                  N
SOLEXAWS1       0       5       1       9156    985     0       1       NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN     BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB     QC                                                                                  N

Need to convert this into Solexa fastq.

Can anyone help me with awk or python or perl script to do this.

Thank you

[Istvan Albert]

I would go with the awk script in the threads that Ram listed

Converting Solexa Reads To Fastq And Identifying Mismatched Bases

Answer 1

[Ram]

Did you check this thread? Or this?

[ChIP]

The perl script at the thread Export2Fastq Conversion and second one I don't know, if it is correct.

[Ram]

You can modify the perl script and map the indices - as far as I can see, you have header info in columns 0 to 7, sequence in col 8 and quality in col 9.