assemble single-read and paired-end read

[morning latte]

Hello all,

I am sorry that my question would is really silly.

I made one library and sequenced in paired-end mode on Illumina GA. The sequencing core provided me with two fastq files, one with paired-end reads and the other with single-end reads. I thought I would get only paired-end reads. Basically, when I run paired-end mode, I am supposed to get both single- and paired-end reads? I heard it is better to use both single- and paired-end reads for assembly since I have both. Then can I just put two input files in velvet command? Could anybody help me be clear with this? Thank you.

[GenoMax]

If the core uses standard illumina CASAVA pipeline data should have been provided as two separate files for the forward and reverse reads (R1, R2 files).

Do you have one file where R1 and R2 reads are interleaved and two additional files where R1/R2 reads are in separate files?

[morning latte]

Thanks for your reply and sorry for my late respond.

I have one fastq file where R1 and R2 reads are interleaved and only one additional file where either R1 or R2 read is in I guess. Because number of reads in the first fastq file is 12,757,578 while 238,314 in the additional fastq file. In fact, I do not understand why the number of reads in the additional file is not the half of the reads of the first file.

[GenoMax]

You will have to check with the core. Do not assume that the sequence in the small file is from your sample till you get an explanation from your core.

For your analysis you should start with the file which has the R1 and R2 reads (should have a /1 and /2 at the end of the fastq sequence ID's designating the respective reads).

I am also not sure why they gave you the reads in interleaved format. That is a bit unusual.

[morning latte]

This really helped. I will check with sequencing core. Thanks again.

[morning latte]

Okay, I learned sequencing core did QC with my files before they gave it to me. They generated one file with R1 and R2 interleaved and the other file where only one member of the pair was retained after filtering. Should I use both files for velvet assembly? Or is it better to use one file with paired-end reads? Thanks a lot for your comments in advance.