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Question: FASTA QC ON GROOMER DATA :
0
gravatar for pinakin76
2.5 years ago by
pinakin76 • 0
pinakin76 • 0 wrote:

PLS COMMENT ON THE DATA
SHOULD IT BE CONSIDERED OR DISCARDED ? SOURCE : RNASeq : SRX273486 File: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR837/SRR837506/SRR837506.fastq.gz

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rna-seq qc groomer galaxy • 824 views
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modified 2.4 years ago • written 2.5 years ago by pinakin76 • 0
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gravatar for Jennifer Hillman Jackson
2.5 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This is your decision, yet I can agree this represents a low quality, short sequence length sample.

Jen, Galaxy team
ADD COMMENT • link written 2.5 years ago by Jennifer Hillman Jackson ♦ 25k
1
gravatar for pinakin76
2.5 years ago by
pinakin76 • 0
pinakin76 • 0 wrote:

Thanks a lot again Jennifer will the data yield significant results on NGS analysis and will it be valid or misleading?
ADD COMMENT • link written 2.5 years ago by pinakin76 • 0
1

one has to decide what can be done with data. Sometime it is the samples that will always provide low level of difficult sequencing. Can you afford to keep on repeating the sequencing or just not do it? It depends on what you decide.

ADD REPLY • link written 2.5 years ago by rob.costa1234 • 10

Quality scores are the metric used to report confidence in base calls. A quality score of 10 means that 1 out of 10 bases may be incorrect. This itself is a very high error rate. If the graph represents all of the sequences in the input file (not just a sample), most would not use it.

More here:

ADD REPLY • link modified 2.5 years ago • written 2.5 years ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for pinakin76
2.4 years ago by
pinakin76 • 0
pinakin76 • 0 wrote:

thanks rob.costa1234
ADD COMMENT • link written 2.4 years ago by pinakin76 • 0
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