De Novo Genome Assembly of SOLiD Data

Question

[waqasnayab]

Hi,

I have SOLiD mate paired data to perform de novo genoem assembly.

I got following error while running SOLiD de novo genome assembly pipeline:

./assemble.pl lane1_T_mp_F3.csfasta lane1_T_mp_F3_QV.qual 130100000 -r3 lane1_T_mp_R3.csfasta -r3qv lane1_T_mp_R3_QV.qual -outdir assembly_lane1 -ins_length 1400 -ins_length_sd 1423

De Novo Assembly Pipeline for SOLiD v.2.0
Copyright (2010-2011) by Life Technologies
***************************************************
Run Reads Sampling.
mkdir -p assembly_lane1;/utils/rsampling lane1_T_mp_F3.csfasta lane1_T_mp_F3_QV.qual 130100000 -outdir assembly_lane1 -r3 lane1_T_mp_R3.csfasta -r3qv lane1_T_mp_R3_QV.qual
sh: /utils/rsampling: No such file or directory
Sampling Failed: 32512

Kindly help me in this regard.

Thanks in advance

Regards,
Waqasuddin Khan.

[h.mon]

This is not a forum post, it is a regular question. You will get more answers if you tag your post correctly. Anyway, your pipeline is not finding rsampling, it is either not installed or installed on a different location.

Answer 1

[sanrrone]

enter to utils directory, and type "make"