ahh!!! right!! It worked!!
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Originally posted by prisnirath View Postthis is the format of my txt MID file
Code:MyMIDs { mid = "MID01", ACGAGTGCGTGTAGCGCGACGGCCAGT, 2; mid = "MID02", ACGAGTGCGTCAGGGCGCAGCGATGAC, 2; mid = "MID03", ACGCTCGACAGTAGCGCGACGGCCAGT, 2; mid = "MID04", ACGCTCGACACAGGGCGCAGCGATGAC, 2; mid = "MID05", AGACGCACTCGTAGCGCGACGGCCAGT, 2; mid = "MID05", AGACGCACTCCAGGGCGCAGCGATGAC, 2; mid = "MID06", AGCACTGTAGGTAGCGCGACGGCCAGT, 2; mid = "MID07", AGCACTGTAGCAGGGCGCAGCGATGAC, 2; }
hth,
Sven
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One more question Sven..
After executing this::
sfffile -s GSMIDs -mcf File2.txt -o reg1 GGDP4G001.sff >MIDyieldR1.txt
Next step is trimming off the MIDs.
when I am trying to do that on a single line command.... it shows error!
sfffile -s GSMIDs -mcf File2.txt -t -o reg1 GGDP4G001.sff >MIDyieldR1.txt
Error: Unable to open accno/trim file: -o
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Originally posted by prisnirath View PostOne more question Sven..
After executing this::
I got some MID sorted SFF files.
Next step is trimming off the MIDs.
when I am trying to do that on a single line command.... it shows error!
There's no need to extra trim your MIDs ... :-)
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Originally posted by prisnirath View Postright! bt i need my final MID trimmed file in sff format...
I haven't yet explored sffinfo but sff2fastq appears to be extracting fastq files from sff files.
If you don't need another format, fine :-) You now have all you need ..
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Originally posted by GraemeFox View PostIn the midconfig.parse file, does anybody know what the default values are for the number of mismatches allowed in each MID?
Code:TITANIUM { mid = "1", "ACGAGTGCGT", 2; mid = "2", "ACGCTCGACA", 2; }
Code:RLMIDs { mid = "RL1", "ACACGACGACT", 1, "AGTCGTGGTGT"; mid = "RL2", "ACACGTAGTAT", 1, "ATACTAGGTGT"; }
Sven
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