Originally posted by arcolombo698
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There is a section in the README about this:
In short, just run:
Code:cutadapt -a AGATCGGAAGAGC -o trimmed.1.fastq.gz reads.1.fastq.gz cutadapt -a AGATCGGAAGAGC -o trimmed.2.fastq.gz reads.2.fastq.gz
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Hi,
I am using cutadapt for removing the adapter sequence. I have 2 adapter sequence.
RNA 5Adapter (RA5)
5 GUUCAGAGUUCUACAGUCCGACGAUC
RNA 3?Adapter (RA3)
5 TGGAATTCTCGGGTGCCAAGG
The 1st one is 5' adapter and 2nd is 3' adapter.
I am using the following command line to remove the adapter seq.
cutadapt -a TGGAATTCTCGGGTGCCAAGG -g GUUCAGAGUUCUACAGUCCGACGAUC input.fastq > output.fastq
Length Distribution I get
Mean sequence length: 32.49 ± 10.53 bp
Minimum length: 16 bp
Maximum length: 51 bp
Length range: 36 bp
Mode length: 51 bp with 2,852,626 sequences
And I found that the 5' adapter has U instead of T. Will that be fine?
I tried replacing U with T GUUCAGAGUUCUACAGUCCGACGAUC > GTTCAGAGTTCTACAGTCCGACGATC and tried removing adapter sequence.
cutadapt -a TGGAATTCTCGGGTGCCAAGG -g GTTCAGAGTTCTACAGTCCGACGATC input.fastq > output.fastq
Length Distribution I get
Mean sequence length: 31.26 ± 11.29 bp
Minimum length: 1 bp
Maximum length: 51 bp
Length range: 51 bp
Mode length: 51 bp with 2,805,271 sequences
I get varied length distribution in both the cases. Which one should I choose..
First is the command that I am using is right??
Kindly let me know.
Thanks in advance.
Regards
Vishwesh
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Originally posted by vishwesh View PostHi,
cutadapt -a TGGAATTCTCGGGTGCCAAGG -g GUUCAGAGUUCUACAGUCCGACGAUC input.fastq > output.fastq
And I found that the 5' adapter has U instead of T. Will that be fine?
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Hi guys
I am using cutadapt 1.3 (I will update to the new version soon), but there is an issue. After trimming the adapter it leaves some empty lines.
Is there a way not to leave empty lines? I don't want to write a script that parses again the file and fixes it.
Thank you in advanceLast edited by foivos; 04-23-2014, 04:43 AM.
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Originally posted by foivos View PostHi guys
I am using cutadapt 1.3 (I will update to the new version soon), but there is an issue. After trimming the adapter it leaves some empty lines.
Is there a way not to leave empty lines? I don't want to write a script that parses again the file and fixes it.
Thank you in advanceLast edited by GenoMax; 04-23-2014, 05:04 AM.
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Originally posted by foivos View PostI am using cutadapt 1.3 (I will update to the new version soon), but there is an issue. After trimming the adapter it leaves some empty lines.
Is there a way not to leave empty lines?
Do not do what is described in the stackoverflow link because it will break your FASTQ file.
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Here is what I get
@BS-DSFCONTROL03:317:C3PGTACXX:2:1101:4054:2147 1:N:0:GCCAAT
TTAGGAAGAGGATAACAATTNGAAACAGTTGCTAAAACTCTATATGC
+
CCCFFFFFGHHHHJJJJJJJ#4AHGGIJIJJIJIJJJJJJJJJJJJJ
@BS-DSFCONTROL03:317:C3PGTACXX:2:1101:4107:2164 1:N:0:GCCAAT
AGTACCCCATGGAC
+
?1?DD?BDA:C;22
@BS-DSFCONTROL03:317:C3PGTACXX:2:1101:4138:2178 1:N:0:GCCAAT
ATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCC
+
CCCFFFFFHHHHHJJJJJJJJJIJJGGJJ:FG-5@D>EEH<?A@/'5<;;B
@BS-DSFCONTROL03:317:C3PGTACXX:2:1101:4219:2179 1:N:0:GCCAAT
+
@BS-DSFCONTROL03:317:C3PGTACXX:2:1101:4242:2199 1:Y:0:GCCAAT
CATACAGGACTCTTTCGAGGCCCTC
+
==>A+2@<+?+?22<A+23)@C+1=
I want it to remove everyting and not leave any gaps...
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You can do that in post-processing. Just put everything on one line using sed:
sed 'N;N;N;s/\\n/\\t/g'
then remove lines containing \t+\t and after change all \t to \n.
Marcel, is version 1.5 up yet? I can only find 1.4.2 as the latest version. If not, when do you anticipate 1.5 to be out?
Thanks!Last edited by sp144; 07-31-2014, 03:37 PM.
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Originally posted by sp144 View PostMarcel, is version 1.5 up yet? I can only find 1.4.2 as the latest version. If not, when do you anticipate 1.5 to be out?
Thanks!
- Adapter sequences can now be read from a FASTA file. For example, write -a file:adapters.fasta to read 3' adapters from adapters.fasta. This works also for -b and -g. This fixes the long-standing issue #33. Note that cutadapt isn't really optimized for trimming dozens or even hundreds of adapters!
- There is now an option --mask-adapter, which can be used to not remove adapters, but to instead mask them with N characters. Thanks to Vittorio Zamboni for contributing this feature!
- U characters in the adapter sequence are automatically converted to T.
- Add the option -u/--cut, which can be used to unconditionally remove a number of bases from the beginning or end of each read.
- When the new option --quiet is used, no report is printed after all reads have been processed.
- When processing paired-end reads, cutadapt now checks whether the reads are properly paired.
- To handle paired-end reads, an option --untrimmed-paired-output was added.
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Hi mmartin,
I'm using the latest version (1.5) and I noticed the format of the info file doesn't seem to match exactly with the documentation on github (https://github.com/marcelm/cutadapt/...ster/README.md). According to it there's supposed to be 8 columns but I only get 7. Column 5 (Sequence of the read before the adapter match) seems to have been removed, yes?
It's not a big deal I don't think as I can recreate the full read by concatenating columns 5 and 6, like the page says ("The concatenation of the fields 5-6 yields the full read sequence."). Or am I missing something?
thanks!
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Originally posted by captainentropy View PostAccording to it there's supposed to be 8 columns but I only get 7.
Column 5 (Sequence of the read before the adapter match) seems to have been removed, yes?
I've tried to clarify all this in the README now. I've also fixed a mistake in the description of how to get the original read sequence: You need to concatenate columns 5-7, not columns 5-6. Hope that helps!
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