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Make --discard-untrimmed work with linked adapters #256
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Hm, that’s how it’s designed at the moment: Only the anchored adapters are required to exist. (You are also using I’ll briefly reiterate what the If you omit the I think you have at least two options:
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This is a duplicate request as #224 is wishing for the same feature. Hopefully, it can be executed as a single command in version 1.15. |
One question: At the end of a read, should partial matches of the 3' adapter be allowed? That is, if the adapter is The biggest problem I usually have with changes like the one in this isse is to decide how the user interface should look. In this case, I think it would be best to not add a command-line option, but to extend the syntax in which adapters are specified. If partial matches are not necessary, one could allow something like this: |
For my use case of extracting CRISPR gRNAs, the partial matches at the 3' side are necessary. I don't know what kind of data Graham has. |
Marcel
Would like to be able to cut adapters in multiple ways something like this.
MyAdapter1TargetSequenceMyAdapter2 ==> TargetSequence
SequenceMyAdapter1TargetSequenceMyAdapter2Sequence ==> TargetSequence
apter1TargetSequenceMyAdapter2Sequence ==> TargetSequence
SequenceMyAdapter1TargetSequenceMyAdapte ==> TargetSequence
apter1TargetSequenceMyAdapte ==> TargetSequence
I am not sure it that is possible?
Best regards
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Yes, that is possible. Exactly the cases you describe are covered if you specify a “non-anchored linked adapter” in the following way: However, what does not work at the moment is to use |
Marcel
In future releases of cutadapt will you be implementing --discard-untrimmed for that use case?
Graham
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I’ve just committed a fix: When you use @DarioS @GrahamHamilton Please let me know if this is what you wanted. Thanks for the feedback; I hope this way cutadapt becomes more useful in CRISPR screening studies! This will be in cutadapt 1.15, which I plan to release this week. |
I have tested the new release of cutadapt and it works as expected on my CRISPR guides dataset. |
Perfect, thanks! |
I am trying to find and trim two adapters from a set of single end reads. I only want reads that have both of the primers present. I am using this "-a adapt1...adapt2$" to define the two adapters and to only trim reads that have both adapters present. However, this results in none of the reads being trimmed. When I omit the "$" at the end of adapt2 the reads are trimmed but reads with only the 5' adapter are included in the output. Am I doing something wrong? Here is the command.
cutadapt -a ATAGCGTTGCTCGAGTACTAACTGGTACCTCTTCTTTTTTTTCTGCAG...CCCTGGTGAATCGCATCG$ -o HiTTs_test_barcodes.fastq HiTTs_test.fastq
And here is my test fasta file
@NS500227:67:HTVFWBGX2:2:12104:24081:17311:ATTACTCG+TAAGATTA ATAGCGTTGCTCGAGTACTAACTGGTACCTCTTCTTTTTTTTCTGCAGNNNSNNNRNNNWCCCTGGTGAATCGCATCGTAGACGCGTATCGAATTCCGCTCGAGATAATCAACCTCTGGATTACAAAATTTGTGAAAGATTGACTG + AAAAAEEEEEEEEEEEEEEAEAEEEEEEEEEEEEAEEEEEEE6EEEEAEEEEE/EE6/EEEEAEEEEE/EEEBBBEEEEEAEEEEEEEEAEAA/EEEEEEEEEE/EE/EEEEEEEEEEEEEEEEE/EEEEEEEEEAEEAAEAAAAA @NS500227:66:HTVFWBGX2:2:12104:24081:17311:ATTACTCG+TAAGATTA ATAGCGTTGCTCGAGTACTAACTGGTACCTCTTCTTTTTTTTCTGCAGNNNSNNNRNNNWCCCTGGTGGGTCGCATCGTAGACGCGTATCGAATTCCGCTCGAGATAATCAACCTCTGGATTACAAAATTTGTGAAAGATTGACTG + AAAAAEEEEEEEEEEEEEEAEAEEEEEEEEEEEEAEEEEEEE6EEEEAEEEEE/EE6/EEEEAEEEEE/EEEBBBEEEEEAEEEEEEEEAEAA/EEEEEEEEEE/EE/EEEEEEEEEEEEEEEEE/EEEEEEEEEAEEAAEAAAAA
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