Dear community,
I am a beginner....trying to use Trimmomatic to clean adaptors/index from my NextSeq500 data. And the Input FASTQ quality scores type is not compatible. Then I would like to convert formats using Groomer, but I do not know which FASTQ quality scores type I should specifiy: Illumina 1.8 or Illumina 1.7-1.3. Or I should not be using Goomer?
Thanks for your help!
Hi,
You could run the tool:
Text Manipulation Concatenate datasets tail-to-head
to merge the files before alignment. Are you sure you want to use Bowtie as aligner and not Tophat/Star/hisat2? Bowtie(2) does not take splice junctions into account.
edit:
You can also merge post-alignment with: NGS: SAMtools Merge BAM Files merges BAM files together
However, I would recommend you to do it prior to alignment as it will save you computational time.
Hello,
The data should be in "fastqsanger" format. This wiki explains how to check if the data is already in that format or not and how to pick groomer settings if you need to use it: https://wiki.galaxyproject.org/Support#FASTQ_Datatype_QA
Best, Jen, Galaxy team
Dear community,
I am now in the process of aligning RNA-seq reads with Bowtie2. My input is a list of 4 fastaq files, one per lane of the sequencing. Is it possible to preset the parameters so that the output from the alignment is a single file?
Thanks you very much in advance
Julia
