Question: removing seqs from paired end read amplicon dataset with mothur
gravatar for lotta.purkamo
4 months ago by
lotta.purkamo0 wrote:

Hiya, I'm trying to make contigs in mothur (v.1.41.1) from my mrDNA-sequenced samples. I've used MrDNA:s Fastq Processor program to get the reads indexed, and made file with mothur make.file command. Everything looks ok at this point, however, I don't have the same number of reads in forward and reverse, as FastQProcessor result.file tells me. For example, Barcodes R1 Seqs R2 Seqs ATTCCGAC 37762 34504

Therefore, when I try make.contigs using the file file, I get an error message "xxx is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding." and mothur crashes because of a segmentation fault.

I've been trying to find a solution by reading help forums, and remove.seqs could be the answer, but I don't understand how to use the command to remove unpaired reads from both R1 and R2. The reads are at this point in fastq-format. Cheers, Lotta

ADD COMMENTlink written 4 months ago by lotta.purkamo0

I think you dont need to look for a solution to remove reads to make R1 and R2 equal again. You should look at why they dont have the same amount of reads anyways. Maybe something went rong with that Fastq Processor program. Were they equal before you processed them with Fastq Processor?

ADD REPLYlink modified 4 months ago • written 4 months ago by gb890

At least the file size is not the same. Any suggestions on how to check whether the raw files R1 and R2 have equal amount of reads?

ADD REPLYlink written 4 months ago by lotta.purkamo0

How to count fastq reads

ADD REPLYlink written 4 months ago by gb890

Thanks! So in the raw files (where all samples are in one file, before using fastqProcessor by MrDNA), same amount of reads, but after separating the reads with the program, different number. So likely there is something fishy going on with fastqProcessor...

ADD REPLYlink written 4 months ago by lotta.purkamo0

Exactly, or you need to change settings or something. Just as far as I know you should not remove reads afterwards to make them the same. That is asking for problems. Good luck

ADD REPLYlink written 4 months ago by gb890
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