trim sequnces

Hello,

The question 1 :
After trimming barcodes and primers, I got the scarp.fasta file. This file will appear “|b”, “|q”, “|bq”, “|h” and “|bqn” in the end of the reads name . I knew the meaning of “|b”, “|q” and “|bq” but I don’t know the meaning of “|h” and “|bqn”. However, I do not know where I can see the meaning of these abbreviations. Please suggest me.

The question 2 :
Is it possibly to read specific primer and barcode which are wrote in oligos file, match with fasta inputfile and then use trim.seqs to trim only barcode, but do not trim primer? Could you please suggest me in trim command or oligos file? I used oligos file which contain primer and barcode, it will trim both of them.

Thanks in advance.

After trimming barcodes and primers, I got the scarp.fasta file. This file will appear “|b”, “|q”, “|bq”, “|h” and “|bqn” in the end of the reads name . I knew the meaning of “|b”, “|q” and “|bq” but I don’t know the meaning of “|h” and “|bqn”. However, I do not know where I can see the meaning of these abbreviations. Please suggest me.

The abbreviations are described in http://www.mothur.org/wiki/Trim.seqs. “bqn” indicates that the read failed because it couldn’t find the barcode (b), it had too low of a quality score (q), and it had an ambiguous base (n). “h” refers to the homopolymer crtieria.

Is it possibly to read specific primer and barcode which are wrote in oligos file, match with fasta inputfile and then use trim.seqs to trim only barcode, but do not trim primer? Could you please suggest me in trim command or oligos file? I used oligos file which contain primer and barcode, it will trim both of them.

If you don’t include the primer sequence in the oligos file it won’t be removed.

Pat