Hello everybody,
My data contains trans-spliced leaders, i.e. short sequences that are attached to the 5 prime end of RNAs after transcription. In the organism I*use, there are about 15 of them known and some transcripts are attached with multiple types. I would like to remove them before de-novo RNA-seq assembly.
Trimmomatic is great but removes reads to the right of the match. In this case I'd like to clip the left part instead.
Cutadapt and Adapterremoval are also good but the "adapters" specification need to be in the command line to my knowledge. That would mean sequentially using one of those tools 15 times to remove the 15 different trans-spliced leaders.
Anyone know another efficient tool that can remove partial/imperfect matches with leading sequences (=to the left)? I*have ~1billion illumina SE short reads.
Many thanks.
Yvan
My data contains trans-spliced leaders, i.e. short sequences that are attached to the 5 prime end of RNAs after transcription. In the organism I*use, there are about 15 of them known and some transcripts are attached with multiple types. I would like to remove them before de-novo RNA-seq assembly.
Trimmomatic is great but removes reads to the right of the match. In this case I'd like to clip the left part instead.
Cutadapt and Adapterremoval are also good but the "adapters" specification need to be in the command line to my knowledge. That would mean sequentially using one of those tools 15 times to remove the 15 different trans-spliced leaders.
Anyone know another efficient tool that can remove partial/imperfect matches with leading sequences (=to the left)? I*have ~1billion illumina SE short reads.
Many thanks.
Yvan
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