Question: Tool in Galaxy for UMIs
0
gravatar for DNAseq
4 weeks ago by
DNAseq0
DNAseq0 wrote:

Hi, I'am new in NGS and not very familiar with data analysis. I'am wondering how can i proceed with data from targeted DNA with UMIs? there is any workflow in Galaxy? What does that mean: 2 read pairs: that does mean paired end sequencing or 2 cycles paired end sequencing? Thank you in advance

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by DNAseq0
0
gravatar for Jennifer Hillman Jackson
4 weeks ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Galaxy tutorials can be found here: https://galaxyproject.org/learn/

There are also public Galaxy Domain-specific servers that include specialized tools/workflows, please see: https://galaxyproject.org/public-galaxy-servers/

When a tool form states something similar to "read pairs" for an input, this nearly always means paired-end reads (two inputs, unless the data is already in a paired collection). Which tool are you looking at if this does not clarify the usage?

Thanks! Jen, Galaxy team

ADD COMMENTlink written 4 weeks ago by Jennifer Hillman Jackson25k
0
gravatar for DNAseq
4 weeks ago by
DNAseq0
DNAseq0 wrote:

Hello Jen, Thank you for your answers. When i got my fastq, adaptor sequences are already trimmed? and data demultiplexed? i have to: upload data on Galxy QC Trimming adaptor, umi traitement? or already trimmed before you got the Fastq? Mapping indel call ... Is that ok for you? Thank you

ADD COMMENTlink written 4 weeks ago by DNAseq0
1

If the adaptors are already trimmed and the demultiplexing done, then yes, map then do the calls. The data source should be able to let you know the status of the data, what artifacts were removed, and other pre-processing steps that were already done. You can also run FastQC to double check - how to do QA/QC is covered in the tutorials.

ADD REPLYlink modified 29 days ago • written 29 days ago by Jennifer Hillman Jackson25k
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