Bisulfite seq file format

[Marisa_Miller]

Hi everyone,
I downloaded some public bisulfite seq data, but I cannot tell what the file format is. The file ends in a .map extension.

This is an example of what the file looks like:

HWUSI-EAS455_0012:8:5:380:1747#0/1 Chr1 19799306 + 0 0 89 89 89 0 0 1 0 62 GGtAATTgTTtAaATgaatTGATTTTTTTTTAAATTTAggtTATTatAagtgAtTGTTGTTT BC;A?BB;B@:<:A@4147CA?BB=C?A??@BBB>BB>1*(BA@>79A7;92?6>@B??BBA
HWUSI-EAS455_0012:1:80:1182:711#0/1 Chr1 19799310 + 0 0 62 62 62 1 13 0 1 63 cTTGTTTAAATGAATTGACTTTTTTTTAAATTTAGGTTATTATAAGTGATTgTTGTTTAGATT +CBABCCC?BCCBBBCCCCCCBCCCCCACCCCCCC?CCCCCACACC@ABCB9BCABCCA>>BB
WUSI-EAS455_0012:8:77:1093:1605#0/1 Chr1 19799317 + 0 0 95 95 95 1 30 1 0 61 AAATGAaTTGATTTTTTTTTAAATTTAGGtTGTTATAAGTGaTTGTTgTTTAGaTTATgtT B@BBB?:@BB@BBBBCCBBB@@ABCB@BB:BB>B?B@?@<@;B>@?@7?>A?@2?@??6;@
HWUSI-EAS455_0012:1:58:152:1944#0/1 Chr1 19799329 - 0 0 86 86 86 0 0 1 0 63 ttttcctcAAatctAAaCTaCCACAAAtAATTATTATCTAAATTaCATcATACAATTtTATAt 458-424;=>+-15==1@B+CCABCB@5BC@@BBB?C@@BCB>B3?@A8BBBCB??A8<CBC9
HWUSI-EAS455_0012:1:65:424:684#0/1 Chr1 19799333 - 0 0 93 93 93 0 0 1 0 61 CCtcAAAtctAAACtACCACAAATAATTATTATCTAAATTACATCATACAATTTTATATCT A?::AB<4:4?A?=;>BCACBBCBCBBABABBBBBCCCABBCC>CCBBCCB>?BCCCCACA

I would like to visulaize the data in IGV. I tried to run the count command in igvtools on this file to see what happened and this is the error message I received:

Unknown file type or sorting not supported for: GSM852836_Ler_1.map
Exception in thread "main" java.lang.NullPointerException
at org.broad.igv.tools.IgvTools.doSort(IgvTools.java:835)
at org.broad.igv.tools.IgvTools.run(IgvTools.java:310)
at org.broad.igv.tools.IgvTools.main(IgvTools.java:192)

It is obvious this file type is not supported, but I am not sure what file type it is. If anyone could help me identify it, that would be a great help!

Thank you,
Marisa

[dpryan]

That's the output from maq (possibly processed by a perl script, I never really used maq myself). I'm sure you can find a maq2sam script somewhere.