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Old 03-08-2010, 08:59 AM   #1
xh4a
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Default novoalign

HI,

I am new to novoalign, when I tried to run it:

./novoalign -f s_1_sequence.txt -F ILMFQ -d hg.ndx

I got the errror:
"' in file s_1_sequence.txt TG is not compatible with minimum quality code '"

Any clue about this error? Many thanks!
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Old 03-08-2010, 08:03 PM   #2
sparks
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Hi,

This message means that the quality values in the file are inconsistent with Illumina Fastq coding format. It may be in older Solexa coding format, could you post the first 20 or so reads from the file.

Colin
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Old 03-09-2010, 05:22 AM   #3
xh4a
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Hi, Colin:

Thanks a lot for reply. Here is part of data:


@HWI-EAS367:1:1:30:1693#0/1
AGCATGAGACAGGGTTAAGGAGNAGCCTCTGTTGAAGAAT
+HWI-EAS367:1:1:30:1693#0/1
aaaaa`a^a`_YWMR_a`ZZ[NDXU[__]^U[[WO\VT]Z
@HWI-EAS367:1:1:30:818#0/1
TGTATCTTCATATATAACAATTNTCAGAGTGAGAATAATA
+HWI-EAS367:1:1:30:818#0/1
a`a\aaaUa^a``^`\^^X]TJDL^YIXQSOOGX___\a\
@HWI-EAS367:1:1:30:1307#0/1
TGTGTGAAAGGCCTTTGCAAATNGCCACAGCAAACTCCCA
+HWI-EAS367:1:1:30:1307#0/1
aa]PXU_Y[SL__WW]T^Za^VDL^W_V]LXYRZ\\^^[W
@HWI-EAS367:1:1:30:40#0/1
AGGGATGAGGTTAGAGAACCACNATTTAGTAACCGCCCTA
+HWI-EAS367:1:1:30:40#0/1
UWT[``V`]VV\`Z_[a]]ab\DIT^a_SQR]`\Z_aaa]
@HWI-EAS367:1:1:30:1020#0/1
ACACACCACACACCTCACACACNCCACACACATACACACA
+HWI-EAS367:1:1:30:1020#0/1
aba`a`a`_]`]^Q[aa`Z_^QDW]OZRRPVV[]ZPRX\[
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Old 03-09-2010, 05:37 PM   #4
sparks
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Hi,

OK, I ran those reads with no problem using the same parameters you had.

Could you tell me what version of Novoalign you are using. It should print as part of header or you can run ./novoalign version

Also could you send at least 20 reads from the file, 80 lines, as Novoalign checks first 20 reads for correct quality values before it starts processing.

Use head -100 s_1_sequence.txt > forcolin.txt

and then email file as an attachment to support at novocraft dot com

Thanks, Colin
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Old 03-10-2010, 04:32 PM   #5
sparks
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Hi Sharon,

The problem is that the file is in DOS format with Carriage Return/Linefeed line separators rather than Linux format with just Linefeed separators. The Carriage return has been picked up as a quality value and is out of range for Illumina fastq format. I'll put a fix in next release of Novoalign so that it ignores carriage returns while processing quality values.
In the meantime you can fix your read file using :

dos2unix < dosformatfile > unixformatfile

Colin
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Old 03-11-2010, 12:52 PM   #6
xh4a
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Default It works

thanks a lot, Colin!!!
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Old 06-15-2010, 10:10 AM   #7
smsm
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I am just wondering if there is a way to search for a specific sequence (20-25 nts) in the bed files. I do not want to only search for the exact sequence. I want to allow mismatches and less than 100% identity.
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