Question: GROOMER ON NEXTSEQ500 DATA
0
gravatar for juliaquingo
21 months ago by
juliaquingo0 wrote:

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!

fastq groomer illumina rna-seq • 537 views
ADD COMMENTlink modified 20 months ago • written 21 months ago by juliaquingo0
1
gravatar for y.hoogstrate
20 months ago by
y.hoogstrate460
Netherlands
y.hoogstrate460 wrote:

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.

ADD COMMENTlink modified 20 months ago • written 20 months ago by y.hoogstrate460

Thank you very much for your help

ADD REPLYlink written 20 months ago by juliaquingo0
0
gravatar for Jennifer Hillman Jackson
21 months ago by
United States
Jennifer Hillman Jackson24k wrote:

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

ADD COMMENTlink written 21 months ago by Jennifer Hillman Jackson24k
0
gravatar for juliaquingo
20 months ago by
juliaquingo0 wrote:

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

ADD COMMENTlink written 20 months ago by juliaquingo0
0
gravatar for juliaquingo
20 months ago by
juliaquingo0 wrote:

Thank you so much for your help and prompt reply!

ADD COMMENTlink written 20 months ago by juliaquingo0
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