Hi SeqA team,
I've hit another road block.
Data information: 16s V3-V4 region, demultiplexed. Illumina, Paired end. PhiX 5%
I've forward, and reverse primer information.
F: CCTACGGGDGGCWGCA
R: GGACTACHVGGGTMTCTAATC
When I try to grep sequences with Forward primer in R1, I get reads from 1k-12k. With all degenerate primer combination.
However, I get less than 10 sequences with reverse primer, degenerate combination on R2.
I tried with ^ (starts), ($)ends with, nothing seems to give me reads for reverse primer.
Tried with reverse complement of reverse primer, no results.
1)
Wouldn't R2 sequences have reverse primers?
2)
I went ahead with forward, and reverse primer information to assemble the reads, with Mothur. I didn't get any output.
When I removed reverse primer information, I managed to get an output of decent file size.
The 16S sequencing was done as the protocol
I've hit another road block.
Data information: 16s V3-V4 region, demultiplexed. Illumina, Paired end. PhiX 5%
I've forward, and reverse primer information.
F: CCTACGGGDGGCWGCA
R: GGACTACHVGGGTMTCTAATC
When I try to grep sequences with Forward primer in R1, I get reads from 1k-12k. With all degenerate primer combination.
However, I get less than 10 sequences with reverse primer, degenerate combination on R2.
I tried with ^ (starts), ($)ends with, nothing seems to give me reads for reverse primer.
Tried with reverse complement of reverse primer, no results.
1)
Wouldn't R2 sequences have reverse primers?
2)
I went ahead with forward, and reverse primer information to assemble the reads, with Mothur. I didn't get any output.
When I removed reverse primer information, I managed to get an output of decent file size.
The 16S sequencing was done as the protocol
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