Problem with RSEQtools

[Aman Mahajan]

I have used soapaligner to align my reads and converted those reads to SAM format using SAMTOOLS..I want to run mrfQuantifier of RSEQtools on these aligned reads but there is some problem with sam2mrf conversion. I am not clear about the command which I can use, in some earlier thread I saw cat command being used but it is generating an executable file..Kindly help if anyone has worked earlier with RSEQtools

THanks.

[bharati]

I am unable to use sam2mrf provided by prebuilt binaries 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.

[zjrouc]

did you solve this problem?