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Old 02-03-2014, 08:24 AM   #1
reema
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Smile FastQC Qualty Control Calculation

Dear All,

I would like to known how quality score is calculated in FastQC for "per base sequence Quality" plot.


Thanks,
Reema Singh
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Old 02-03-2014, 10:18 AM   #2
blakeoft
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The "Help > Contents... > Analysis Modules > Per Base Sequence Quality" section should answer your question. This plot gives a lot of different kinds of statistical data including mean (blue line), inter-quartile range (yellow boxes) and median (red line).
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Old 02-04-2014, 12:18 AM   #3
simonandrews
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The quality scores themselves aren't calculated by FastQC - they're taken directly from the fastq files and are added by the base calling software of the sequencing platform. They're basically a measure of the signal to noise for each base call. The exact implementation will vary depending on the sequencing platform (and they normally don't tell you exactly how it's done). If you want to know more about the meaning of the scores you can look at the quality section of the wikipedia fastq article which describes this pretty well.
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Old 02-04-2014, 07:52 AM   #4
reema
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Hello Simon and blakeoft

Thanks, It helps.

Regards
Reema Singh
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Old 02-13-2014, 07:13 AM   #5
reema
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Post Trinity-Duplicate removal

Dear All,

I am using trinity for transcriptomics assembly. I have few queries:-

1) have two condition(Control and Treated) and each condition has 4 replicates. so if I merge these .fq files together, how the generated assembly from this merged .fq file would be better than the assembly generated from single(using only one replicate) sample?

2) Do I need to remove duplicates from individual fastq file before merging or after merging them together?

3) I saw there is a script "fasta_remove_duplicates" in the trinity folder. So is there any chance that "In-silico-normalization" in trinity take care of these duplicate reads?

I would appreciate any explanations.
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Old 02-13-2014, 07:18 AM   #6
GenoMax
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Quote:
Originally Posted by reema View Post
Dear All,

I am using trinity for transcriptomics assembly. I have few queries:-

1) have two condition(Control and Treated) and each condition has 4 replicates. so if I merge these .fq files together, how the generated assembly from this merged .fq file would be better than the assembly generated from single(using only one replicate) sample?

2) Do I need to remove duplicates from individual fastq file before merging or after merging them together?

3) I saw there is a script "fasta_remove_duplicates" in the trinity folder. So is there any chance that "In-silico-normalization" in trinity take care of these duplicate reads?

I would appreciate any explanations.
Reema: Consider moving this to a new thread since it is not related to your original query. Many people are not going to see this question otherwise.
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Old 02-13-2014, 07:37 AM   #7
reema
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Quote:
Originally Posted by GenoMax View Post
Reema: Consider moving this to a new thread since it is not related to your original query. Many people are not going to see this question otherwise.
Thanks,

Now I posted as a new thread.
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