Hello,
I received a dataset of reads that are supposed to have the following format:
bases (1-3) = 3bp fingerprint (I know what this sequence should be)
bases 4-28 = 25bp read
bases 29-36 = 8bp adapter sequence (I know what this sequence should be)
The fingerprint is OK and the 1st 3 bases where thus trimmed.
However, in many cases, the adapter sequence is a few bases longer or shorter than 8bp. Thus, trimming 8bases from the end results in reads that lack a few bases or that contain a few bases from the adapter...
In some reads, I can't find the adapter sequence... it seems like I have 25+8 bases of genomic sequence, but I'm not sure about that...
Is there a way to qualitatively trim the reads from the end, removing all (but only) the adapter sequence?
Thanks a lot for your help
-a-
I received a dataset of reads that are supposed to have the following format:
bases (1-3) = 3bp fingerprint (I know what this sequence should be)
bases 4-28 = 25bp read
bases 29-36 = 8bp adapter sequence (I know what this sequence should be)
The fingerprint is OK and the 1st 3 bases where thus trimmed.
However, in many cases, the adapter sequence is a few bases longer or shorter than 8bp. Thus, trimming 8bases from the end results in reads that lack a few bases or that contain a few bases from the adapter...
In some reads, I can't find the adapter sequence... it seems like I have 25+8 bases of genomic sequence, but I'm not sure about that...
Is there a way to qualitatively trim the reads from the end, removing all (but only) the adapter sequence?
Thanks a lot for your help
-a-
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