Illumina 1.9 read lengths and trimming

[jellybaby83]

Hi all.

I have had a genome of a bacteria I am working with sequenced by my universities sequencing facility. It has been sequenced on a Miseq and I have paired-end reads. I have received from them the raw fastq files and files that they have trimmed using sickle and scythe.

I have run all the files through fastqc and have this has told me that the read lengths are as follows.

Untrimmed_1 = 236 - 251
Untrimmed_2 = 35 - 251
Trimmed_1 = 20 - 251
Trimmed_2 = 20 - 251

It is my understanding that, at least the untrimmed, reads should be the same length?
I also received a few warnings on all files for Kmer content, but I think this might be due to my organism having a low GC content (~25%).

I would like to know if these read lengths are acceptable? Should I look at trimming them to the same length? Is there any perticually good software for this?

To be honest, I have very little idea what I need to do. If anyone has any good links to papers or other information about triming files etc. I would really appreciate that.

Thanks.

[GenoMax]

Do you know if the data was processed (before the trimming) on MiSeq itself/BaseSpace or after the run using bcl2fastq/CASAVA?

[jellybaby83]

Unfortunately not. All I received was an email with the files that basically said thanks for your custom.

[GenoMax]

I have a feeling that some trimming occurred during the pre-processing of the data (either on MiSeq/BaseSpace) and what you received was not original full length reads. It probably does not really matter since you would have removed those bases yourself during post-processing. One issue that can result in shorter reads is that you had inserts that were shorter than what you thought they were.

If you are looking to assemble the data then SPAdes is a good option.

[GenoMax]

There are plenty of threads for various trimming programs. BBDuk is the simplest option.

[jellybaby83]

Thanks for your help.

[relipmoc]

Hi all.

I have had a genome of a bacteria I am working with sequenced by my universities sequencing facility. It has been sequenced on a Miseq and I have paired-end reads. I have received from them the raw fastq files and files that they have trimmed using sickle and scythe.

I have run all the files through fastqc and have this has told me that the read lengths are as follows.

Untrimmed_1 = 236 - 251
Untrimmed_2 = 35 - 251
Trimmed_1 = 20 - 251
Trimmed_2 = 20 - 251

It is my understanding that, at least the untrimmed, reads should be the same length?
I also received a few warnings on all files for Kmer content, but I think this might be due to my organism having a low GC content (~25%).

I would like to know if these read lengths are acceptable? Should I look at trimming them to the same length? Is there any perticually good software for this?

To be honest, I have very little idea what I need to do. If anyone has any good links to papers or other information about triming files etc. I would really appreciate that.

Thanks.

If you have raw fastq files where all the reads are of the same length, you may use skewer for adapter trimming.

See http://www.biomedcentral.com/1471-2105/15/182/ for your reference.