Entering edit mode
9.5 years ago
carvin900
•
0
Hi,
Sorry in advance for my beginner level in bioinformatic. I need to do analysis of illumina reads paired end. The starting files I have are: fwd.fastq , reverse.fastq and mapping file.txt.
In the sequences files, there are several samples with different barcodes (barcodes with different lengths) and different primers (3 different set of primers). I tried so far to:
- I extracted barcodes with
extract_barcodes.py --bc1_len X --bc2_len X
(where is x is the length of the barcode). I have barcodes of length 4,5,6,7 and 8 so I did 5 times this command with different lengths - I merged the reads1.fastq and reads2.fastq output files from 1) for each barcodes length.I had 1,78% in general of non-merging sequences.I also asked to get a
fastjoin.join_barcodes.fastq
file. - I tried to do split_libraries_fastq.py with the merged sequences and the
fastjoin.join_barcodes.fastq
file. But then I get over 1 900 000 reads non associated to barcodes out of 2 500 000 total reads.
If someone could help me I would be really glad!
Vincent
Hi Geek_y,
thanks for the rapid answer. I am fairly new in bioinformatic and my research lab is mostly using Qiime, so haven't heard of CASAVA. Also, our local server is based on Qiime. Would it be possible to launch commands from Qiime to CASAVA? Thanks for your help!
Vincent
Thanks for your help Geek_y, I found out my mistake. There was a switch of two bases in our primer sequence registered and the primer sequence in the reads. Now all is doing fine. I only have done merging and already split_libraries.py. Thanks again!