[galaxy-user] FASTQ joiner

Hi all, Has anyone used FASTQ joiner with a file containing multi-mapped reads? I'm pretty sure i have reads mapped to several locations and i don't know what this tool does with it? will it locate the right map according to the paired read? will it use the first read location and ignore the rest

Re: [galaxy-user] FASTQ joiner

Lilach: This tool works on unaligned reads in fastq format before they are mapped. It is useful for merging mates together into a single read for QC processing, filtering, and trimming. Thanks! anton On Wed, Sep 11, 2013 at 4:34 AM, lilach noy lilach...@gmail.com wrote: Hi all, Has anyone

Re: [galaxy-user] FASTQ joiner fails to join PE data.

Hello, The FASTQ Joiner tool is currently being updated to work with the newer sequence Id format. The progress of this change can be tracked here: https://bitbucket.org/galaxy/galaxy-central/issue/677/update-joiner-tool-to-work-with-casava-18 Meanwhile, quality filtering can be done on

[galaxy-user] FASTQ joiner fails to join PE data.

Hi, I have HiSeq2000 paired end sequence data in two separate FASTQ files. I need to filter the low quality scored sequences from my data to have a good assembly. So I decided to join the PE reads and then filter the low quality sequences in Galaxy. To do this first I groomed the data using

Re: [galaxy-user] FASTQ joiner

Hi Matthew, Are you by chance using sequences with the newer CASAVA 1.8+ formatting? For example: @HWI-ST765:83:D091AACXX:1:1101:1202:2130 If so, this tool is known to not work correctly (it skips over the IDs). We do consider it a priority to update the tool. You can track our progress by

[galaxy-user] fastq joiner problem

Hi, I am trying to join two groomed fastq files from a paired-end Illumina read using the fastq joiner tool. The drop-down menus correctly identify the groomed fastq files, but after cranking for a few minutes the tool produces empty output: FASTQ joiner on data 5 and data 4emptyformat: