FastQC, Trimming, Overall QC (initial) #1

J.v.N. · 2021-02-09T13:02:09+01:00

J.v.N. commented

2021-02-09 13:02:09 +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)

J.v.N. added 1 commit 2021-02-09 13:02:10 +01:00

FastQC, Trimming, Overall QC (initial) 3d7c9e3b1c

H.C. Donker commented

2021-02-09 15:06:15 +01:00

See my review comments.

J.v.N. added 1 commit 2021-02-09 15:16:32 +01:00

Test change 58bd93171c

J.v.N. 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

rnaseq/step2_trim/snippet.sh Outdated

						
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				#!/bin/bash

H.C. Donker commented

2021-02-09 14:57:35 +01:00

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`.

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rnaseq/step2_trim/snippet.sh Outdated

						
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				#!/bin/bash

				#SBATCH --job-name=trimming

H.C. Donker commented

2021-02-09 15:03:47 +01:00

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?

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rnaseq/step2_trim/snippet.sh Outdated

						
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				dir_trimmed_fastq="$(pwd)/fastq/trimmed"

				dir_trimmed_fastq_reports="$(pwd)/fastq/trimmed/reports"

				adapter_3p="TGGAATTCTCGG" # is _R1

H.C. Donker commented

2021-02-09 14:56:26 +01:00

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

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rnaseq/step2_trim/snippet.sh Outdated

						
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				          adapter_seq=$adapter_5p

				        fi

				        echo ">>Trimming with sequence ${adapter_seq}"

				        trim_galore \