[prisnirath]

ahh!!! right!! It worked!!

[prisnirath]

thank you!

[sklages]

this is the format of my txt MID file

Go for something like this:

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;
}

.. change the names and/or mismatches to whatever is approbiate ..

hth,
Sven

[prisnirath]

One more question Sven..

After executing this::

sfffile -s GSMIDs -mcf File2.txt -o reg1 GGDP4G001.sff >MIDyieldR1.txt

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!

sfffile -s GSMIDs -mcf File2.txt -t -o reg1 GGDP4G001.sff >MIDyieldR1.txt
Error: Unable to open accno/trim file: -o

[prisnirath]

what is a typical format of trim file?? I want to trim off my MIDs

[sklages]

One 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!

'sfffile' splits the input SFFs according to their MIDs. It also shifts the trimpoints in the sff file accordingly. So if you use e.g. 'sffinfo' to extract the sequences (or sff2fastq), then it will skip the MID sequence. Offsets are shifted from 5 (key sequence) to something around 14 ...

There's no need to extra trim your MIDs ... :-)

[prisnirath]

right! 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.

[sklages]

right! 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.

-> you get SFF (sfffile outputs just SFF)

If you don't need another format, fine :-) You now have all you need ..

[prisnirath]

thank you

[GraemeFox]

In the midconfig.parse file, does anybody know what the default values are for the number of mismatches allowed in each MID?

[sklages]

In the midconfig.parse file, does anybody know what the default values are for the number of mismatches allowed in each MID?

For standard titanium, have a look at the number just before the ';', e.g. 2

TITANIUM
{
        mid = "1", "ACGAGTGCGT", 2;
        mid = "2", "ACGCTCGACA", 2;
}

For RapidLibs have a look at the number in the middle, e.g. 1

RLMIDs
{
        mid = "RL1",   "ACACGACGACT", 1, "AGTCGTGGTGT";
        mid = "RL2",   "ACACGTAGTAT", 1, "ATACTAGGTGT";
}

Also have a look at the docs, "4.7.2 The MIDConfig.parse File".

Sven