[mira_talk] Splitting paired-end reads
- From: Lionel Guy <guy.lionel@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 17 Mar 2009 18:43:53 +0100
Hi,
First, I really like mira, and this mailing-list! Happy to make my
first post here ;)
I know this is a list for mira, and my problem regards rather
sff_extract, but since Bastien has written the sff_extract part that
deals with paired-end reads, I thought I might give a try here...
I'm trying to parse a sff file and to get correct paired-end reads
info. sff_extract works fine, but returns 99% of partial linker
matches (.pl reads), and maybe 1% of correct pairs, whereas I know I
have more. I turned some debugging print in sff_extract, and saw that
there are some regular discrepancies between the correctedseq and
maskedseq, but I can't really make sense of that.
The linker sequence is:
TCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACG
Below is a part of the output:
Any idea of what could be wrong? Any relationship with the very recent
update of SSAHA2? (I have 2.3)
Thanks for your help!
molev166:/seq/bpe3/readSorting/tmp$: ~/bin/sff_extract -o test -
l ../../originalData/linker.fasta ../../originalData/sff/FLVI58L05.sff
Working on '../../originalData/sff/FLVI58L05.sff':
Creating temporary sequences from reads in '../../originalData/sff/
FLVI58L05.sff' ... done.
Searching linker sequences with SSAHA2 (this may take a while) ... ok.
Parsing SSAHA2 result file ... done.
Converting '../../originalData/sff/FLVI58L05.sff' ... Partial hits in
FLVI58L05FSYNS
tcagGGTTTGCACGCCTTCGACGCAACACCATCGTGAGTTTCCGATAGCTCGCATCGAAATTTCTCAAACAGTACTCTGTATTCATAGACAGAGAGACCGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGATAAACGTTTTCGATAAAAAGGACAACGTATGTTGTAGTAAAATTTTTTGAAGTTTCTAAAAActgagactgccaaggcacacaggggatagg
####GGTTTGCACGCCTTCGACGCAACACCATCGTGAGTTTCCGATAGCTCGCATCGAAATTTCTCAAACAGTACTCTGTATTCATAGACAGAGAGACCGTA
##################################ACGATAAACGTTTTCGATAAAAAGGACAACGTATGTTGTAGTAAAATTTTTTGAAGTTTCTAAAAA
##############################
########################AACACCATCGTGAGTTTCCGATAGCTCGCATCGAAATTTCTCAAACAGTACTCTGTAT
##########################################################################AAAGGACAACGTATGTTGTAGTAAAA
##################################################
Partial hits in FLVI58L05FRQEW
tcagTTGTCCATGAAGCTCTTGAAGAAAGTGGAAATAAAGCTCTATACTATATACCACAGTCGTCATAACAAGTATCAAAGCATAAATAGAAAAACTCAGAAGAGAAGGAAAAGGATTTATCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGAAAATAAACTGGCCCCTCCATTTAAACAGGTTGActgagactgccaaggcacacaggggataggnn
####TTGTCCATGAAGCTCTTGAAGAAAGTGGAAATAAAGCTCTATACTATATACCACAGTCGTCATAACAAGTATCAAAGCATAAATAGAAAAACTCAGAAGAGAAGGAAAAGGATTTA
##########################################AAAATAAACTGGCCCCTCCATTTAAACAGGTTGA
################################
########################GAAAGTGGAAATAAAGCTCTATACTATATACCACAGTCGTCATAACAAGTATCAAAGCATAAATAGAAAAACTCAG
################################################################################################################################
Partial hits in FLVI58L05FP2BE
tcagTTTCAAGCTCTTTTTCAACAGCGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGAATGGCTTGTGCAAGTTCATCTGTTGATAAAGTCCCCAAAATTGCCAAAGCAACTTTAGCCCCCACACCAGGCACATTTTGCAGCAAGCAAAACCACTCTTGTTCTGCTCTTGTAGCAAAACCAAAAAGGCGAATAGCGTCTTCACGAACATGTGTTTCAATAAAGAGACTTATACTCTCACCAAGAGCGGGTAAAGAAGGACGCAGCCGATTTGACACAAAAACCACATAACCCACACCGTGAACATTTACAAGGATATGATCATCAAAGATATGTTCAAGAGTCCCCTTTTAATTACCAATCActgagactgccaaggcacacaggggataggn
####TTTCAAGCTCTTTTTCAACAGCGTA##################################ACGAATGGCTTGTGCAAGTTCATCTGTTGATAAAGTCCCCAAAATTGCCAAAGCAACTTTAGCCCCCACACCAGGCACATTTTGCAGCAAGCAAAACCACTCTTGTTCTGCTCTTGTAGCAAAACCAAAAAGGCGAATAGCGTCTTCACGAACATGTGTTTCAATAAAGAGACTTATACTCTCACCAAGAGCGGGTAAAGAAGGACGCAGCCGATTTGACACAAAAACCACATAACCCACACCGTGAACATTTACAAGGATATGATCATCAAAGATATGTTCAAGAGTCCCCTTTTAATTACCAATCA###############################
###################################################################################CATCTGTTGATAAAGTCCCCAAAATTGCCAAAGCAACTTTAGCCCCCACACCAGGCACATTTTGCAGCAAGCAAAACCACTCTTGTTCTGCTCTTGTAGCAAAACCAAAAAGGCGAATAGCGTCTTCACGAACATGTGTTTCAATAAAGAGACTTATACTCTCACCAAGAGCGGGTAAAGAAGGACGCAGCCGATTTGACACAAAAACCACATAACCCACACCGTGAACATTTACAAGGATATGATCATCAAAGATATGTTCAAGAGT###################################################
============================================
Lionel Guy
Thunmansgatan 25, SE-75421 Uppsala
phone: +46 (0)18 245596
mobile: +46 (0)73 9760618
email: guy.lionel@xxxxxxxxx
============================================
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