Parclip suite usage

Question

[pandikannan4]

I am trying to use Parclip suite (Rockefeller university) for analysing my PAR-CLIP data. I can process my files upto the stage of collapsed fasta format. After that, while using the perl script analyse_parclip.pl, repeated errors come while bowtie indexing.

bowtie --sam -v 2 -p 8 -f -k 20 ./Human_transcriptome_reference/genome /home/usr/bin//dat1_GC.fa > .///home/usr/bin//dat1_GC_res.anno_bwt_t
sh: 1: cannot create .///home/usr/bin//dat1_GC_res.anno_bwt_t: Directory nonexistent

Can anyone please help me to solve this error. I have checked for the directories and it is placed fine.

Answer 1

[finswimmer]

Hello,

do you know how the file path syntax on unix systems work?

• ./ indicates to start the path from your current working directory.
• multiple / are not useful

So I guess the correct syntax in your case is:

$ bowtie --sam -v 2 -p 8 -f -k 20 ./Human_transcriptome_reference/genome /home/usr/bin/dat1_GC.fa > /home/usr/bin/dat1_GC_res.anno_bwt_t

Be careful: This will create or if the file exists overwrite the file dat1_GC_re.anno_bwt_t in the folder /home/usr/bin/

• Is there really a user called usr on the system?
• Should this file be placed in a bin folder?
• The output of bowtie is usually a samfile.

fin swimmer