Trimming sequencing primers from reads

Question

[barzilayrom1]

Hi all,

I am going through a work-flow for analysis of paired-end reads data obtained from next-seq 500 (based on a published protocol) and it is noted that the sequencing primer should be trimmed from the reads. I wonder why should you do that, since as far as I understand the sequencing primer shouldn't even be a part of the read, or am I wrong?

I would really appreciate your feedback!

Thanks

[GenoMax]

Sequencing primer should not be part of the reads. Perhaps the workflow meant to say adapters instead.

[barzilayrom1]

Thanks! I thought so too, wonder though if it could happened by chance or due to error in base calling

Answer 1

[Fahad]

bash: java.jar/Trimmomatic-0.39/trimmomatic-0.39.jar: No such file or directory

[Pierre Lindenbaum]

what is that ? is it a comment ? is it a question ?