Hi.
While i was looking at some FASTQC results, i realized that in test_1.fq file FASTQC didn't find any adapter or over-expressed sequence. Although on the other hand FASTQC found illumina's adapter on test_2.fq file.
1) I thought that illumina's machine at the end of the process, removes automatically all adapter sequences while it seems that it doesn't
2) Also i realized that there are reads constituting by sequences like this:
Is that possible ? Is it possible two or more adapter sequences merged together and then read start ? How that bias occurred ?
3) Finally is there any way of getting out the 100% of the reads ? Nothing less and nothing more. Just the reads. I'm asking because it finally seems that inside the "reads" there are sequences that have nothing to do with real reads.
Any tool/article/video will be helpful.
Thank you.
While i was looking at some FASTQC results, i realized that in test_1.fq file FASTQC didn't find any adapter or over-expressed sequence. Although on the other hand FASTQC found illumina's adapter on test_2.fq file.
1) I thought that illumina's machine at the end of the process, removes automatically all adapter sequences while it seems that it doesn't
2) Also i realized that there are reads constituting by sequences like this:
Code:
adapterSequence--adapterSequence--readDequence
3) Finally is there any way of getting out the 100% of the reads ? Nothing less and nothing more. Just the reads. I'm asking because it finally seems that inside the "reads" there are sequences that have nothing to do with real reads.
Any tool/article/video will be helpful.
Thank you.
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