Problem with Velvet.

Question

[El Niño]

Dear all,

I need to do genome assembly and I chose to try Velvet. However, after reading this tutorial and follow the steps, I came across some problems:

1. I cannot run shuffleReads.pl
2. when I run velveth directory 21 -fastq -short unpaired.fastq -shortPaired paired.fastq, Linux replied Segmentation fault.

I Googled those errors but found no solutions.

Can anyone help me with this?

Many thanks,

The-Anh.

[Ram]

I cannot run shuffleReads.pl

That is a vague statement - we do not know if the script won't execute (which means there is an error when you try to run it, not "I cannot run") or if someone is holding your wrist stopping you from typing the command (which fits "I cannot run" but is not something we can help with). Please be more specific.

[JC]

It's hard to know the error source without details, at least you should copy-paste your commands and errors, also indicate OS. The segmentation fault error is commonly generated because your analysis cannot allocate all the memory.

Answer 1

[El Niño]

Thank you both. I figured that out myself. The 1st problem is that I need to download shuffleReads.pl from the official website (because my version does not include it). The 2nd one I just modified some parameters and it worked.

Again, thank you for your prompt replies. I highly appreciate it.