[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

[GraemeFox]

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

[prisnirath]

thank you

[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]

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]

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]

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

[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

[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]

thank you!

[prisnirath]

ahh!!! right!! It worked!!

[sklages]

i have got my SFF files...true!!
I got a MID file in csv format.
And I have parsed it to a tab-delimited file.
My question is while using ::
sfffile -s SPC_MIDs -mcf MyMIDfile.parse MY_SFF_FILE.sff

MyMIDfile.parse :: MID file (right??)

...what file format shoud I be using for parsing it to its acceptable format?

I took suggestions from the thread http://seqanswers.com/forums/showthread.php?t=10825
and I am getting error!!
sfffile -s Y -mcf file2.txt -o reg1 GGDP4G001.sff >MIDyieldR1.txt
Error: Invalid file format 2: file2.txt

Have you read my post? I have described the format you should use for sfffile to split SFFs according to their MIDs ...

Just another ... the output of sfffile is a new SFF; no need to redirect (to a text file) ..

hth,
Sven

[prisnirath]

ACGAGTGCGTGTAGCGCGACGGCCAGT
ACGAGTGCGTCAGGGCGCAGCGATGAC
ACGCTCGACAGTAGCGCGACGGCCAGT
ACGCTCGACACAGGGCGCAGCGATGAC
AGACGCACTCGTAGCGCGACGGCCAGT
AGACGCACTCCAGGGCGCAGCGATGAC
AGCACTGTAGGTAGCGCGACGGCCAGT
AGCACTGTAGCAGGGCGCAGCGATGAC
;
;
;

this is the format of my txt MID file

[prisnirath]

i have got my SFF files...true!!
I got a MID file in csv format.
And I have parsed it to a tab-delimited file.
My question is while using ::
sfffile -s SPC_MIDs -mcf MyMIDfile.parse MY_SFF_FILE.sff

MyMIDfile.parse :: MID file (right??)

...what file format shoud I be using for parsing it to its acceptable format?

I took suggestions from the thread http://seqanswers.com/forums/showthread.php?t=10825
and I am getting error!!
sfffile -s Y -mcf file2.txt -o reg1 GGDP4G001.sff >MIDyieldR1.txt
Error: Invalid file format 2: file2.txt

[sklages]

Thank you!!
I understand it now!
But still a little confused...
I have got my MID files in CSV format and I have converted this file into txt, tab delimited and fasta file.
Which format should I be using here?

Now, I am confused :-)

You should have your data in SFF files, your MIDs in roche conform "parse" format, e.g.

CUSTOM_MULTIPLEX
{
    mid = "MID4000", "ACACGT", 0;
    mid = "MID4001", "ACGTAC", 0;
    mid = "MID4002", "ACTGCA", 0;
    mid = "MID4003", "AGAGTC", 0;
}

where '0' stands for the allowed number of mismatches for a MID to be still valid.

If you use "Rapid Libraries" you might want to check 3' ends as well,

RLMIDs
{
    mid = "RL1",   "ACACGACGACT", 1, "AGTCGTGGTGT";
    mid = "RL2",   "ACACGTAGTAT", 1, "ATACTAGGTGT";
    mid = "RL3",   "ACACTACTCGT", 1, "ACGAGTGGTGT";
    mid = "RL4",   "ACGACACGTAT", 1, "ATACGTGGCGT";
}

Again, the number stands for allowed mismatches in MID recognition.
The second sequence in this format has no influence on splitting, it just gets trimmed (if found). Splitting is exclusively done on MIDs present at the 5' end.

hth,
Sven