Re: [galaxy-user] Metagenomic filtering

2013-09-19 Thread Scott Tighe
Gerald 16s is basically useless for identification to genus. Since I started sequencing 16s in 1992, I have come to realize that without sequencing the full 1540 bases, it is generally misleading, and even than, it is not accurate enough to nail genus on more than 1/2 the cases. However,

Re: [galaxy-user] Identifying Tags - Galaxy Question

2013-09-19 Thread Jennifer Jackson
Hi Dominique, Glad that helped. And yes, you can merge many file types that are text-based with the tool 'Text Manipulation - Concatenate datasets. Sometimes you will need to convert to format tabular first, and then back to the desired format (fasta, gtf, etc.) after. Take care, Jen

[galaxy-user] 3' adapter trimming using FASTX-toolkit clipper

2013-09-19 Thread Hoang, Thanh
Hi all, I am analyzing miRNA sequencing now. My data is 51bp, single -ended and ~5 M reads. I want to remove the adapter sequences from the reads before mapping to the genomes/known miRNA database. My 3' adapter sequence is : 5-AGATCGGAAGAGCACACGTCT-3. I found that many reads only contain part of

Re: [galaxy-user] 3' adapter trimming using FASTX-toolkit clipper

2013-09-19 Thread Jennifer Jackson
Hi Thanh, Just enter the whole adapter sequence. The tool will match what is found in the input sequence and clip. The help graphic on the Clip form itself illustrates this - only one adapter is entered (can be entered) but a variable length is clipped from the input to produce the output.

Re: [galaxy-user] 3' adapter trimming using FASTX-toolkit clipper

2013-09-19 Thread Jennifer Jackson
Thanh, To hopefully be clearer, the part matched is clipped (whole or partial, and there is even some tolerance for low-frequency mismatches). I would suggest taking a few sequences out and running the tool on them to try it out. You could test for both length and mismatch constraints this