FASTXtoolkit adapter trimming

[earonesty]

Thanks I'll give it a try

I noticed at your site a tool for stitching pe reads called fastq-join. It doesn't appear to be available yet. When will it be?

You can just grab the code... it's POSIX C++ and should compile easily:

http://code.google.com/p/ea-utils/source/browse/trunk/clipper/fastq-join.c

g++ -O3 fastq-join.c -o fastq-join

[Mark]

Thanks I'll give it a try

I noticed at your site a tool for stitching pe reads called fastq-join. It doesn't appear to be available yet. When will it be?

[earonesty]

We rewrote a lot of fastx's toolkit stuff, and posted it here: https://code.google.com/p/ea-utils/. It attempts to do things like adapter removal, trimming, etc... without as much configuration by detecting presence of adapters located in a common file.

[gghl]

Hi Mark,

Based on my understanding, the fastx_clipper first finds the adaptor seqeunce you give and then trims off adaptor and nucleotide sequenes after the adaptor. I think fastx_clipper is designed for removeing adaptor after the insert seqeunces. And this is why in your test fastq file, reads of test 1, 2 and 4 were considered as adaptor-only reads.

I think if what you want is to remove 5' end adaptor in front of the insert seuqences, the fastx_trimmer might be able to help.

Best wishes,
gghl

[maasha]

Oh, and if you want to trim multiple adaptors either process the fastq file several times or just use remove_adaptor multiple times:

read_fastq -i test.fastq |
remove_adaptor -a CCTTAAGG -r before |
remove_adaptor -a GACACCTGG -r after

SCORES: HHHHHHHHHHHHHHHHHHHH
SEQ: AAAAAAAAAAGGGGGGGGGG
SEQ_NAME: test1
SEQ_LEN: 20
ADAPTOR_POS: -1
---
SCORES: HHHHHHHHHHHHHHHHHHHH
SEQ: AAAAAAAAAGGGGGGGGGGG
SEQ_NAME: test2
SEQ_LEN: 20
ADAPTOR_POS: -1
---
SCORES: HHHHHHHHHHHHHHHHHHHHHHHHHHHH
SEQ: AGAGAGAGAGAGAGAGAGAGAGAGAGAG
SEQ_NAME: test3
SEQ_LEN: 28
ADAPTOR_POS: -1
---
SCORES: [[[[[[[[[[[
SEQ: TTGACGTGATC
SEQ_NAME: test4
SEQ_LEN: 11
ADAPTOR_POS: 11
---

M

[maasha]

I can't help you with the FASTX toolkit, but here is how to do it with Biopieces (www.biopieces.org).

read_fastq -i test.fastq | remove_adaptor -a CCTTAAGG -r before
SCORES: HHHHHHHHHHHHHHHHHHHH
SEQ: AAAAAAAAAAGGGGGGGGGG
ADAPTOR_POS: 0
SEQ_LEN: 20
SEQ_NAME: test1
---
SCORES: HHHHHHHHHHHHHHHHHHHH
SEQ: AAAAAAAAAGGGGGGGGGGG
ADAPTOR_POS: 0
SEQ_LEN: 20
SEQ_NAME: test2
---
SCORES: HHHHHHHHHHHHHHHHHHHHHHHHHHHH
SEQ: AGAGAGAGAGAGAGAGAGAGAGAGAGAG
ADAPTOR_POS: -1
SEQ_LEN: 28
SEQ_NAME: test3
---
SCORES: [[[[[[[[[[[[[[[[[[[[
SEQ: TTGACGTGATCGACACCTGG
ADAPTOR_POS: 0
SEQ_LEN: 20
SEQ_NAME: test4
---

Use grab to get the entries that were trimmed and finally use write_fastq to create a new file:

read_fastq -i test.fastq | remove_adaptor -a CCTTAAGG -r before | grab -e 'ADAPTOR_POS>=0' | write_fastq -o test_trimmed.fastq -x

Cheers,


Martin

[Mark]

Hi All

I recently downloaded the FASTX toolkit and tried to use it for trimming fastq reads of adapter sequences. This did not work, the tool simply discarded any reads containing adapter sequences though this is not seemingly its function according to the documentation. I wrote to the help contact for the tool but recieved no response (see below for details). Has anyone used this tool for this purpose successfully?

Thanks for your help

Mark

#############################################
Hello

I recently downloaded the FASTX toolkit (fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2) and attempted to use the fastx_clipper tool. I created a test fastq file (3 of the four sequences contain the default adapter CCTTAAGG):

@test1
CCTTAAGGAAAAAAAAAAGGGGGGGGGG
+test1
HHHHHHHHHHHHHHHHHHHHHHHHHHHH
@test2
CCTTAAGGAAAAAAAAAGGGGGGGGGGG
+test2
HHHHHHHHHHHHHHHHHHHHHHHHHHHH
@test3
AGAGAGAGAGAGAGAGAGAGAGAGAGAG
+test3
HHHHHHHHHHHHHHHHHHHHHHHHHHHH
@test4
CCTTAAGGTTGACGTGATCGACACCTGG
+test4
[[[[[[[[[[[[[[[[[[[[[[[[[[[[

And then executed the command (as shown on FASTX toolkit website)

-bash-3.2$ fastx_clipper -v -i test.fastq -a CCTTAAGG
@test3
AGAGAGAGAGAGAGAGAGAGAGAGAGAG
+test3
HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Clipping Adapter: CCTTAAGG
Min. Length: 5
Input: 4 reads.
Output: 1 reads.
discarded 0 too-short reads.
discarded 3 adapter-only reads.
discarded 0 N reads.

As you can see, the three reads that contain the adapter are discarded as “adapter-only reads” which (in my way of looking at things) they are not nor are they too short (default <=5) after any trimming. What is going on here? Does this tool actually trim reads or only discard them if they are found. If the former would you please tell me what I am doing incorrectly? Also if the former, is it possible to supply the tool with multiple adapters to trim?

Thanks for your help

Mark