Velvet-Insert Size

[VNou]

Hello i am trying to assembly Staphylococus from the pair end library that i found in this site:
http://www.ebi.ac.uk/ena/data/view/SRR022868

and 2 short jumping libraries find at

http://www.ebi.ac.uk/ena/data/view/SRR022865


I want to ask 2 questions:

1)In the run of velvetg i have to provide the insert length. How can i find it?

2)Do i have after shuffling the short jumping libraries to reverse them?

Thank you a lot

[cliffbeall]

Hello i am trying to assembly Staphylococus from the pair end library that i found in this site:
http://www.ebi.ac.uk/ena/data/view/SRR022868

and 2 short jumping libraries find at

http://www.ebi.ac.uk/ena/data/view/SRR022865


I want to ask 2 questions:

1)In the run of velvetg i have to provide the insert length. How can i find it?

2)Do i have after shuffling the short jumping libraries to reverse them?

Thank you a lot

For the insert length, if you don't specify it velvet will calculate it automatically. Alternatively you might map some reads to a reference genome or some assembled contigs and calculate it yourself..

To the second question, with the latest version, you no longer need to shuffle (use the -separate flag). If they are the Illumina-type mate pairs (from circularization) you do need to reverse complement the second read.

[VNou]

I found this command:
shuffleSequences_fastq.pl shortjump_1.fastq shortjump_2.fastq - | fastx_reverse_complement > shortjump.fastq

This command first shuffles and the reversed the output of the shuffle or it reverses the second read and then it shuffles?

[cliffbeall]

You only want to run reverse complement on the shortjump_2.fastq file. The command you have will reverse complement both reads.

Also like I said, with the latest velvet you no longer need the shuffleSequences script.