solexa output files | s_*_seq.txt vs. s_*_sequencece.txt

[lajoieb]

Hi All,

Quick question...

Why would I be seeing more reads in the s_*_seq.txt files in the Bustard directory that I see in the s_*_sequence.txt files in the Gerald directory (fastq).

i.e.
wc -l s_*_seq.txt (normal read file)
8301558 total

wc -l s_*_sequence.txt (fastq)
25885740 s_8_2_sequence.txt

There should be 4 lines for each read in the fastq files but I am not seeing these numbers line up. Anyone know anything about this?
Are some sequences excluded from the fastq files compared to the normal sequence files?

Thanks!

[kmcarr]

The *_seq.txt files in the Bustard directory include the sequence of every cluster (read). The *_sequences.txt files in the GERALD directory only include the passed filter reads.

[lajoieb]

Ah ok!
That makes perfect sense then.

Appreciate the explanation.

bryan

[Torst]

wc -l s_*_sequence.txt (fastq)

To count the number of reads in a FASTQ file, you can use grep in -c (counting) mode:

grep -c '^\+' *_sequence.txt

s_6_sequence.txt:4525658
s_7_sequence.txt:4485601
s_8_sequence.txt:4099309

Note you can't match on '@' as that is a valid quality value (Q=0), wherease '+' is not used in Illumina FASTQ. This is easier than dividing by four in your head... although the shell can help us there too:

echo $[ `wc -l < s_6_sequence.txt` / 4 ]

4525658

Enjoy