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.
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.
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