FastQC, Trimming, Overall QC (initial) #1

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Jos van Nijnatten merged 6 commits from P300299/system_genetics:master into master 2021-02-15 16:20:22 +01:00

Yea, so... I have added

  • a script for FastQC (To be checked/altered by Rene, checked by Cancan)
  • a script for Trimgalore (To be checked/altered by Aurore, checked by Hylke)
  • a couple of scripts for QC-ing the outcome of the alignment (counts table) (To be checked by Tatiana)
Yea, so... I have added - a script for FastQC (To be checked/altered by Rene, checked by Cancan) - a script for Trimgalore (To be checked/altered by Aurore, checked by Hylke) - a couple of scripts for QC-ing the outcome of the alignment (counts table) (To be checked by Tatiana)
Jos van Nijnatten added 1 commit 2021-02-09 13:02:10 +01:00
Owner

See my review comments.

See my review comments.
Jos van Nijnatten added 1 commit 2021-02-09 15:16:32 +01:00
Jos van Nijnatten requested review from H.C. Donker 2021-02-09 15:40:48 +01:00
H.C. Donker requested changes 2021-02-09 15:51:04 +01:00
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#!/bin/bash
Owner

Perhaps write some instructions how to use. E.g., you need samples.csv.

Perhaps write some instructions how to use. E.g., you need `samples.csv`.
P300299 marked this conversation as resolved
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#!/bin/bash
#SBATCH --job-name=trimming
Owner

Maybe a general question, do we want to:

  • provide am entire script that processes an entire batch of samples, or
  • do we want to focus on the core of trimming (only trim_galore/Trimmomatic command with options), and remove all the for loops and if-else statements?
Maybe a general question, do we want to: - provide am entire script that processes an entire batch of samples, or - do we want to focus on the core of trimming (only `trim_galore`/`Trimmomatic` command with options), and remove all the for loops and if-else statements?
P300299 marked this conversation as resolved
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dir_trimmed_fastq="$(pwd)/fastq/trimmed"
dir_trimmed_fastq_reports="$(pwd)/fastq/trimmed/reports"
adapter_3p="TGGAATTCTCGG" # is _R1
Owner

Does this depend on sequencing machine/library type? If so, specify.

Does this depend on sequencing machine/library type? If so, specify.
P300299 marked this conversation as resolved
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adapter_seq=$adapter_5p
fi
echo ">>Trimming with sequence ${adapter_seq}"
trim_galore \
Owner

I though we were going to use trimmomatic?

I though we were going to use trimmomatic?
P300299 marked this conversation as resolved
Jos van Nijnatten added 2 commits 2021-02-10 13:43:01 +01:00
Jos van Nijnatten removed review request for H.C. Donker 2021-02-12 09:52:10 +01:00
Jos van Nijnatten requested review from T. Karp 2021-02-12 09:52:26 +01:00
Jos van Nijnatten changed title from WIP: FastQC, Trimming, Overall QC (initial) to FastQC, Trimming, Overall QC (initial) 2021-02-12 09:53:08 +01:00
Jos van Nijnatten added 1 commit 2021-02-15 12:54:43 +01:00
T. Karp approved these changes 2021-02-15 16:12:19 +01:00
Jos van Nijnatten added 1 commit 2021-02-15 16:18:39 +01:00
Jos van Nijnatten merged commit e2206cbc39 into master 2021-02-15 16:20:22 +01:00
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Reference: GRIAC/system_genetics#1
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