RSeqtools, bed2interval conversion

[labrat73]

Greetings,

Has anyone worked with the utility in RSeqtools that converts .bed format to interval? I have tried it and find that strand information is missing from my output file. See example below:

BED_1 chr20 . 123292 126094 1 123292 126094
BED_2 chr20 . 251843 256677 1 251843 256677
BED_3 chr20 . 256662 257502 1 256662 257502
BED_4 chr20 . 257721 257933 1 257721 257933
BED_5 chr20 . 257954 259040 1 257954 259040

Any advice on what's going on here would be greatly appreciated!

Many thanks!

labrat73

[bharati]

I am unable to use sam2mrf of RSEQtools, can anybody pls help?
The command I tried was "sort -r file.sam | sam2mrf > file.mrf"
as specified in the manual for the alignment file generated by tophat but it didnt work.

please reply soon.

[GenoMax]

I am unable to use sam2mrf of RSEQtools, can anybody pls help?
The command I tried was "sort -r file.sam | sam2mrf > file.mrf"
as specified in the manual for the alignment file generated by tophat but it didnt work.

please reply soon.

Bharati,

Is the sam2mrf command in your $PATH? If not, you need to provide full directory path to that command when you try to run that command.

sort -r file.sam | /path_to_this_file/sam2mrf > file.mrf

If this does not address the "error" you got then please provide the exact error message you are getting.

Generally there is no need to post the same question in multiple threads.

[bharati]

Ya i specified the path for both the sam2mrf script and that of the alignment file, even though it didnt work and terminates with the error "Invalid SAM entry: ñ`"