Can you see what i got problem??

Question: Can you see what i got problem??

14 months ago by

cucucucoco • 0 wrote:

I did uproading file through EBI homepage about NCBI Geo dataset SRR 5682257 &5682258. [EBI SRA: SRX2917412 File: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR568/007/SRR5682257/SRR5682257.fastq.gz] and it was convert using FASTQ Groomer Tool (convert between various FASTQ quality formats) at NGS: QC and manipulation. because first file is gz file that are compressed file. next, i did click FastQC Tool (Read Quality reports), so that i see Quality control of this dataset.

unfortunately, per tile sequence quality and sequence Duplication levels got X. i am user who use Galaxy tool first time for analysis NCBi dataset. so i am poor.

In this case, Is this data sets already finished Trimming by original uproader?? so am i just have to start analysis alingment using Bowtie ? other wise, IS this dataset' Quality very low?

what i have got problem T-T... please help me.

quality control fastqc galaxy • 382 views

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modified 14 months ago by Jennifer Hillman Jackson ♦ 25k • written 14 months ago by cucucucoco • 0

14 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello

Reviewing these FAQs and tutorials will help you to understand the workflow for QA and data prep (plus more).

In summary, it is best to upload data, run FastQC, review the results to determine the quality score format, convert with the Groomer tool (only if needed) or directly assign the fastqsanger datatype, run FastQC again if you ran Groomer, assess quality, Trim/filter as needed with (Trimmomatic, Trim Galore!), FastQC again to review how the QA changed the data (you might want to try a few different settings and compare to find the best options for your specific data), then proceed to map steps and downstream analysis.

All tutorials https://galaxyproject.org/learn/
- NGS data prep tutorial including help for interpreting and acting on FastQC results https://galaxyproject.org/tutorials/ngs/
- Data QA is also included in many of the targetted analysis tutorials, for example, those that cover Variant Analysis, Metagenomics, RNA-seq, and others
All FAQs https://galaxyproject.org/support/
- With these first few FAQs explaining the technical details of loading and prepping sequence data: https://galaxyproject.org/support/#getting-inputs-right-

Hope this helps! Jen, Galaxy team

ADD COMMENT • link written 14 months ago by Jennifer Hillman Jackson ♦ 25k

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