Weird SOLiD data format?

[ajc]

Hi,

I have some data that I know was generated using SOLiD, but I don't recognize the format. It looks almost like a colorspace fastq file, but not quite, like this:

>1739_884_912_F3,2_-11523929.1,13.34
T32202001123212121221020202001222022
>1791_1330_1088_F3,3_-46239737.1,17.29
T03213011011311212110322211030010033
>465_1064_1221_F3,9_86102047.0,20.91
T30122123101011101201231020122131323
>2275_505_1405_F3,1_-98592059.3,16.34
T20220110202103221120011021100003000
>1886_592_994_F3,9_116983194.2,18.91
T13100232120223122002121002000120233

The first line is apparently
>(bead-info),(chr)_[- if on neg strand](coordinate, Mm 9).(#mismatches),[Quality_score]

Can anyone tell me what format this is and how I can convert it to typical fastq format?
Thanks!!

[anjana.vr]

Looks like the file is in .ma format. Its something that SOLiD uses frequently. I have this description of the format.

>bead_ID, sequence#_signedCoordinate_#mm_alignmentSize .

Also you can convert .ma to gff and then to SAM. If thats useful take a look at the following thread

http://seqanswers.com/forums/showthread.php?t=4426&highlight=matogff

Hope that helps.

[Brugger]

Hi

you cannot go from ma -> fastq as the ma file does not contain any colour quality information. What you need is the original .qual file that was used with the mapping. What you probably want is the original csfasta and qual file, otherwise you have to trim the read names in the .ma file.

Also be careful with colour space fastq files as different programs expect the format slightly different.

Hope this helps.