[mmartin]

It will be really helpful if you could provide that code. Do you know how SHRiMP and Mosiak assembler deal with it?

Dear Neel,
I'm sorry to say that the code I had in mind was only for the old MAQ output files and it won't work with SAM files. I looked at it a bit, but it is not straightforward to get it to work with SAM files. As far as I know, SHRiMP is much better at dealing with colorspace. I cannot say anything about Mosaik.

[nntao]

consideration of paired ends

Nice job creating this tool!
one suggestion: be nice to be able to work with paired end reads together to improve accuracy especially for reads contain short partial adaptors, since if one read contain adaptor the other end should contain adaptor as well.

[naluru]

Thanks, Marcel. No problem. I will try to work around it.

Neel

[robs]

robs: cutadapt was developed for SOLiD and 454 data and also works with Illumina reads.

cutadapt is focused on command-line users who have a data file from a second-generation sequencing machine and want to simply remove one or more know adapter sequences from that file. There is probably some overlap in functionality to the tools you mention. TagClean and SeqClean were published after I have implemented cutadapt, and SeqTrim was unknown to me. Also, SeqClean and SeqTrim seem to be primarily for the analysis of Sanger sequencing data. I cannot say how easy it is to get them to work with second-generation data. SeqTrim, for example, seems to not be able to cope with FASTQ files.

Thanks for the answer. It might be useful to perform some run time comparisons. Also, I think non of the previous tools were designed for pair-end read data and I agree with nntao that this would be a nice feature to see in cutadapt.

[mmartin]

This is interesting. I have only some experience with paired-end data. How would the data look like? Would one expect that the adapter starts at the same position in both reads?

[nntao]

Trimming adaptors from paired-end reads

It depends on how the paired-end sequencing libraries are prepared, in particular, whether adaptor/primers are introduced in the process. In a general case, you'll have molecuales like the following that are fed to the sequencer (sometimes the adaptor are after the sequencing primers, other times the there could be just sequencing primer):


----adaptor1SAMPLEDNA2rotpada
--->adaptor1SAMPLEDNA2rotpadaremirp # F read obtained with 2 bp adaptor underlined
----adaptor1SAMPLEDNA2rotpada<- # R read with a 2 bp from adaptor too


---primerSAMPLEDNAremirp
-------->SAMPLEDNAremirp # read obtained



When trimming short adaptors down to 2 bp, you may over-trim reads that are with ends like the adaptor/primer (~~ 1/16 chance). But if both Forward and Reverse reads contain the 2 bp adaptor, they are likely from the adaptor because the SAMPLEDNA fragment is short (thus both reads would contain adaptors).

Again, thanks for you hard and nice work!

[mmartin]

Thanks for the explanation ("rotpada" is nice :-) ). I cannot promise that I'll implement this, but I've added it as an enhancement request to the issue tracker. It would also be helpful if someone could provide me with a few actual paired-end reads with adapters. A SRA accession number would also be ok.

[mmartin]

Hello,

I'd like to announce that cutadapt 0.9.5 has been released. Please see the cutadapt homepage for the release announcement and the changelog. Please also note that the alignment algorithm was improved slightly in this release.

[chadn737]

Thanks, this has been a wonderful tool by the way.

[mghita]

Hi, I am trying to use cutadapt to trim the adapter in some illumina reads, the adapter is on the first position. The output still contains the adapter. What am I doing wrong?

cutadapt -a N ~/Desktop/pr/reads1.fq -o ~/Desktop/pr/reads.fq

Also, is there any option in bwa that trims the first base of the read (or an adapter)?

[mghita]

I have a problem using cutadapt. The output file still contain the adapter. What am I doing wrong?

cutadapt -a N ~/Desktop/pr/reads1.fq > ~/Desktop/pr/reads.fq


When I use the program, it removes the adapter, but when I save it in an output file, it has the adapter.

[Torst]

I have a problem using cutadapt. The output file still contain the adapter. What am I doing wrong?
cutadapt -a N ~/Desktop/pr/reads1.fq > ~/Desktop/pr/reads.fq
When I use the program, it removes the adapter, but when I save it in an output file, it has the adapter.

"-a N" means your adaptor sequence is a single "N" letter? Is that what you intended?

[mghita]

"-a N" means your adaptor sequence is a single "N" letter? Is that what you intended?

Initially, that was what I was intended, but I have discovered that other reads include a series of N's, so now I am interested in removing the reads that have N's inside. cutadapt did not work for that either.

Also, I would like to know if anyone has any method of eliminating the first (few) and last (some) bases from the reads?

[Torst]

Initially, that was what I was intended, but I have discovered that other reads include a series of N's, so now I am interested in removing the reads that have N's inside. cutadapt did not work for that either.
Also, I would like to know if anyone has any method of eliminating the first (few) and last (some) bases from the reads?

You should be able to write a trivial perl/python/C program to remove reads with N in them?

If not, perhaps the FASTX toolkit could be used: http://hannonlab.cshl.edu/fastx_toolkit/

[lmilne]

Is it possible to have an option added to cutadapt to mask adapter sequences rather than to discard or trim reads?