Trimming SOLiD adapters

Question

[kimmitzka]

Hi,

Which tool should I use to trim adaptors in SOLiD files? It seems that trim-galore can not be used in SOLiD. Thanks a lot!

I used this command:

trim_galore -q 20 --phred33 --length 20 ERR791838.fastq.gz --gzip -o ./cleandata/trim_galoredata/

But it didn't works. And I got an error

File seems to be in SOLiD colorspace format which is not supported by Trim Galore (sequence is: 'T22...23...31..200..203..210..113...10....0....2...')! Please use Cutadapt on colorspace files separately and check its documentation!

Sincerely,

kimmi

[lieven.sterck]

well, the messages suggests to use Cutadapt. Did you try that one?

[kimmitzka]

It seems that Cutadapt need an adaptor file. But I don't have it.

[Ram]

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[kimmitzka]

okay, thank you!

[h.mon]

Due to the 2 base encoding system, SOLiD is mainly useful when mapping to a reference genome, and in this case, there is no need to trim adapters, as they will be soft-clipped from the alignment.

I am not sure, but I think Cutadapt dropped support for SOLiD reads, so you will need to use an old Cutadapt version, in case you really need to trim the adapters.

[kimmitzka]

Hi, you mean it is not necessary to trim adaptors in SOLiD sequencing?

[h.mon]

If you are mapping to a reference genome (the situation where SOLiD reads are most useful), there is no need to trim adapters, as the mapping software will soft-clip these regions from the alignment.

In case you want to assemble something, such as a transcriptome, you do need to trim the adapters - but note it is a bad idea to use SOLiD reads in assembly, as:

1. (in my experience) they have poor quality,
2. most programs can't deal with colorspace reads, and you would need to convert them to basespace, defeating the main purpose of SOLiD technology.