Question: Cutadapt need adaptor sequence input
0
gravatar for tran_tim
2.1 years ago by
tran_tim10
tran_tim10 wrote:

I use cutadapt on galaxy to trim my adaptors for my fastq files. Does the program find a default adapter or do I have to enter in the sequence of my adapters I want to trim. I am getting this output without entering any known adaptors.

This is cutadapt 1.11 with Python 2.6.6 Command line parameters: --format=fastq --adapter=Dummy-Adapter (do not use me)=TGTAGGCC --adapter=Dummy-Adapter (do not use me)=TGTAGGCC --error-rate=0.1 --times=1 --overlap=3 --output=/var/local/galaxy/galaxy-dist/database/files/029/dataset_29799.dat /var/local/galaxy/galaxy-dist/database/files/029/dataset_29757.dat Trimming 2 adapters with at most 10.0% errors in single-end mode ... Finished in 10.05 s (32 us/read; 1.89 M reads/minute).

=== Summary ===

Total reads processed: 315792 Reads with adapters: 7782 (2.5%) Reads written (passing filters): 315792 (100.0%)

Total basepairs processed: 42220496 bp Total written (filtered): 42054262 bp (99.6%)

=== Adapter Dummy-Adapter (do not use me) ===

Sequence: TGTAGGCC; Type: regular 3'; Length: 8; Trimmed: 7782 times.

No. of allowed errors: 0-8 bp: 0

Bases preceding removed adapters: A: 24.2% C: 20.5% G: 17.1% T: 38.2% none/other: 0.0%

Overview of removed sequences length count expect max.err error counts 3 5260 4934.2 0 5260 4 1096 1233.6 0 1096 5 3 308.4 0 3 6 82 77.1 0 82 7 1 19.3 0 1 11 2 4.8 0 2 89 2 4.8 0 2 90 2 4.8 0 2 91 417 4.8 0 417 92 4 4.8 0 4 93 2 4.8 0 2 111 1 4.8 0 1 113 1 4.8 0 1 114 1 4.8 0 1 115 1 4.8 0 1 116 16 4.8 0 16 117 877 4.8 0 877 118 6 4.8 0 6 131 7 4.8 0 7 132 1 4.8 0 1

=== Adapter Dummy-Adapter (do not use me) ===

Sequence: TGTAGGCC; Type: regular 3'; Length: 8; Trimmed: 0 times.

ADD COMMENTlink modified 2.1 years ago by Jennifer Hillman Jackson25k • written 2.1 years ago by tran_tim10
0
gravatar for Jennifer Hillman Jackson
2.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The tool trims some items automatically (aka poly-A tails) plus adaptors. There is a configuration file that will hold specified adaptors if you are running this on your own local/cloud. See the tool in the Tool Shed (http://usegalaxy.org/toolshed) and the manual for more details.

Best, Jen, Galaxy team

ADD COMMENTlink written 2.1 years ago by Jennifer Hillman Jackson25k
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