This is a test version of Biostars. For the public version, visit https://www.biostars.org.
determining SJ with SOAPsplice

hy guyz. im newbie to NGS data analysis and using SOAPaplice to determine SJ for paired end reads. I have successfuly built an index with all its 12 output files. However, I am unable to align my sequences as Im getting an error message 

**cannot open bwtCodeFile!**

can someone kindly help me to resolve this problem????

the command line I am using for this purpose is as follows:

/data/sata4/SOAPsplice-v1.10/bin/soapsplice -d /data/sata4/SOAPsplice-v1.10/indexsoap/soap_index -1 /data/sata4/SRR95_Qt_1P.fq -2 /data/sata4/SRR95_Qt_2P.fq -o soapsplice_align -f 2
alignment
• 1,196 views • link
updated by Heath • Heath • written by blooming.daisy333 • blooming.daisy333

1 answer

I think you can solve it by append ".index" to your prefix of reference files "soap_index"

• 1 views • link
written by Heath • Heath

Log in to answer this question.

More posts like this
  • building index with HISAT2
    written by blooming.daisy333 • blooming.daisy333
    I am newbie to linux and NGS. Whle trying to build an index with hisat2 for my project, im getting following error: "Error: could not …
  • Tophat tool error
    written by blooming.daisy333 • blooming.daisy333
    im using tophat too determine splice junction but encountering a strange error. [2018-04-16 12:43:28] Beginning TopHat run (v2.1.1) ----------------------------------------------- [2018-04-16 12:43:28] Checking for Bowtie Bowtie …