[Oliviervg]

Hello, and thank you for this great program.

I have a stupid question, but I don't understand what does "trim" mean and what does "clip" mean ? What's the difference between them ?
Is trim a synonym for "cut" ?

[Oliviervg]

Can someone answer to my stupid question please ?
What the difference between clip and trim ?
Thank you

[Oliviervg]

I know my question should seem stupid for a native english speaker, but I still not understand the difference between trimming and clipper ...
Maybe they are synonyms, and we can use both terms in each case ?

[westerman]

I know my question should seem stupid for a native english speaker, but I still not understand the difference between trimming and clipper ...
Maybe they are synonyms, and we can use both terms in each case ?

Trim usually means an algorithmic determination of where to clip off sequences. E.g., trim all bases from 5' end where the quality value is 20 or less (Q20) in a running total of 4 bases.

Clip is usually a hard and fast rule. E.g., clip 15 bases off of the 5' end.


But, yes, trim and clip could also be considered synonyms.

[earonesty]

But, yes, trim and clip could also be considered synonyms.

Yep. They are synonyms, and are used inconsistently.

Personally, I say "clip", when I mean "looking for adapters or other sequences and removing them off the ends of reads", and "trim" when I mean "looking for qualities/base skew" and removing them off the ends of reads. (fastx-toolkit and fastq-mcf seem to use it this way.)

[relipmoc]

Hi Mark,

Recently I've written a software tool named skewer which is dedicated to the adapter trimming task of Illumina paired-end reads. It's very easy to use. I've compared the result of skewer and that of fastq-mcf. The overall gained uniquely-mapped read-pairs of skewer is higher than that of fastq-mcf in my case.

Below is the related statistics of using fastq-mcf and skewer:
run 1 (using a popular adapter trimmer fastq-mcf):
70252244 reads; of these:
70252244 (100.00%) were paired; of these:
66639175 (94.86%) aligned concordantly 0 times
3099256 (4.41%) aligned concordantly exactly 1 time
513813 (0.73%) aligned concordantly >1 times
6.27% overall alignment rate

run 2 (using skewer):
5136192 reads; of these:
5136192 (100.00%) were paired; of these:
192115 (3.74%) aligned concordantly 0 times
4264035 (83.02%) aligned concordantly exactly 1 time
680042 (13.24%) aligned concordantly >1 times
97.01% overall alignment rate
---- trimming information of skewer ----
70676932 read pairs processed
29547 ( 0.04%) degenerative read pairs filtered out
17685 ( 0.03%) short read pairs filtered out after trimming by size control
65493508 (92.67%) empty read pairs filtered out after trimming by size control
5136192 ( 7.27%) read pairs available; of these:
1285606 (25.03%) trimmed read pairs available after processing
3850586 (74.97%) untrimmed read pairs available after processing

you may download skewer from https://sourceforge.net/projects/skewer/

Cheers,
Hongshan

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

[debjit_ray]

FASTQC on my small RNA sequences identifies several overrepresented sequences. It might be because of the adapter sequences. I do a trimming for the adapter ('ACTA') using the command
>fastx_clipper -C -v -i SRR519779.fastq -Q 33 -a ACTA -o SRR519779_trimmed.fastq
The out put for this is:
Clipping Adapter: ACTA Min. Length: 5 Clipped reads - discarded. Input: 4484151 reads. Output: 4440775 reads. discarded 0 too-short reads. discarded 0 adapter-only reads. discarded 0 clipped reads. discarded 43376 N reads.

Seems there is no effect of this trimming, the FASTQC shows similar results on the trimmed sequence.
Can the adpator be just 4 nucleotides? Am I doing something wrong? Please suggest.