jstjohn/SeqPrep — Issue #4: always discards reads
Author: earonesty
Created: 2012-02-22 19:41:01+00:00
State: open

I have single-end data. I tried:

./SeqPrep -L 30 -A TCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -f 3-02.fq -r 3-02.fq -1 x.gz -2 y.gz

./SeqPrep -L 1 -A TCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -f 3-02.fq -r 3-02.fq -1 x.gz -2 y.gz

And I get the same results:

Pairs Processed: 100003
Pairs Merged: 0
Pairs With Adapters: 14104
Pairs Discarded: 14104

It seems to be discarding always, regardless of the length of the remaining sequence.

EXAMPLE... this should clip 3 reads:

@chr1_126402405_126402916_0:0:0_0:0:0_f0/1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGT
+
2222222222222222222222222222222222222222222222222222222222222222222222
@chr1_190335492_190335960_1:0:0_4:0:0_f1/1
TATCATATTTTGGACTTGCATGTGGACTGTAGCCCCTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCG
+
2222222222222222222222222222222222222222222222222222222222222222222222
@chr1_203905302_203905767_0:0:0_0:0:0_f2/1
AGGCATAGGTTGCAGTGGGCCGAGATCGTGCCACTGCACTCCAACATGGGTGACAGAGTGAGACCCCGTC
+
2222222222222222222222222222222222222222222222222222222222222222222222
@chr1_43121485_43121960_1:0:0_1:0:0_f3/1
ATCCTTTGACTCAGTCCATTCTTGCGAATTTGTTTTCTGGAGTAATTCAAAAGAAGAAAAGAACTACATG
+
2222222222222222222222222222222222222222222222222222222222222222222222
@chr1_220744965_220745411_2:0:0_0:0:0_f4/1
TTTATCAAAGGATAACTTAAAGAACAGCTACTTTGCTGGCTGCAGTGGTGTTTCCCTGTGGTCTCAGCTA
+
2222222222222222222222222222222222222222222222222222222222222222222222
@chr1_77131320_77131830_1:0:0_4:0:0_f5/1
TTTCCGAATTAAGTTTCATAAGAATTCTGTATAGTTTTTTAAAAATTGAATTTTGATTGTTTTTTGGAAA
+
2222222222222222222222222222222222222222222222222222222222222222222222
@chr1_21795162_21795580_1:0:0_2:0:0_f6/1
TTGGGTGTCTTCTCCCCAGTCCCTGGCCCCACATCTTCTGCCACAAACGTCAGCATGGTGGTATCTGCCG
+
2222222222222222222222222222222222222222222222222222222222222222222222
@chr1_137758389_137758826_0:0:0_0:0:0_f7/1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
2222222222222222222222222222222222222222222222222222222222222222222222
@chr1_116182085_116182584_1:0:0_1:0:0_f8/1
AAAAAAAAAACAAAAAAACATGCCGGGGGACCTGGGCAAGATGGCTGAATAGGAACAGCTCCAGTATGCA
+
2222222222222222222222222222222222222222222222222222222222222222222222
@chr1_78447528_78448102_1:0:0_1:0:0_f9/1
AAAGGTTAATGAAAAAGATAAATGTAATAGAAGAACTGATTATCTAAATATATGATCCATCGTGTAGGGA
+
2222222222222222222222222222222222222222222222222222222222222222222222