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Hello,
I was wondering if there was a way to remove a particular sequence from all reads from Illumina output that is fairly straightforward. I do not have a bioinformaticist resource available to help me work with my data. I used a cDNA amplification of a small amount of RNA and did Illumina paired-end sequencing. A very small % of my reads are aligning to the genome. I found out that the cDNA amplification we are using can cause concatemers at the 5' end of the amplified cDNA. We are getting reads that are aligning to odd genomes including some plants and think the concatemers may be causing issues with alignment to the bovine genome. Is there any way to remove a known custom sequence from all reads in an entire Illumina dataset before moving forward with alignment? Thank you in advance for any help.
ccard28
I was wondering if there was a way to remove a particular sequence from all reads from Illumina output that is fairly straightforward. I do not have a bioinformaticist resource available to help me work with my data. I used a cDNA amplification of a small amount of RNA and did Illumina paired-end sequencing. A very small % of my reads are aligning to the genome. I found out that the cDNA amplification we are using can cause concatemers at the 5' end of the amplified cDNA. We are getting reads that are aligning to odd genomes including some plants and think the concatemers may be causing issues with alignment to the bovine genome. Is there any way to remove a known custom sequence from all reads in an entire Illumina dataset before moving forward with alignment? Thank you in advance for any help.
ccard28
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