s_*_export.txt VS s_*_sequence.txt

[zhuj]

Hi All,

What's the relationship between the s_*_export.txt and s_*_sequence.txt ?

I previously supposed the export file is the alignment of the sequence file, but the export file contains more reads than the sequence file.

Then I supposed the sequence file is the filtered results based on the export file, and I counted the total number of unique hits, "N0:N1:N2", "NM" and "QC". There is no consistent sum among these numbers.

Anybody knows the exact relationship between the two files?

I appreciate any helps from you guys.

Jiang

[Simon Anders]

My guess would be that the sequence file contains only the sequences that passed the chastity filter while the xport file contains all reads. Could you check that by counting the number of 'Y's in the chastity column?

Simon

[HESmith]

Simon is correct; the sequence file contains the reads that pass filter. Also, depending upon the configuration, the sequence file format can vary (options are fastq, fasta, or scarf).

-Harold

[zhuj]

Yeah, the number of "Y" in the filtering column is the same as the number of reads in sequence file.

Thanks Simon and Harold.

Jiang

[lmf_bill]

I guess sequence file is consistent with *.sorted.txt file

[HESmith]

The sorted file contains those reads that pass the chastity filter AND uniquely align to the reference genome.

-Harold