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Originally posted by bharati View PostI 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.
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.
Code:sort -r file.sam | /path_to_this_file/sam2mrf > file.mrf
Generally there is no need to post the same question in multiple threads.
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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.
Leave a comment:
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RSeqtools, bed2interval conversion
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!
labrat73Tags: None
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