Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Th gc count dev #15

Open
wants to merge 8 commits into
base: main
Choose a base branch
from
Open

Th gc count dev #15

Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
276bb8b
add gc calc and reporting
tanyabyte Jul 15, 2024
d0fdca1
adding gc-percentage calculation and reporting
tanyabyte Jul 17, 2024
52aadf8
Update workflow test.yml
tanyabyte Jul 22, 2024
b060bcd
Update workflow test.yml
tanyabyte Jul 22, 2024
d4ad3f6
Modified test.yml
tanyabyte Jul 23, 2024
6ae9deb
Update test.yml
tanyabyte Jul 23, 2024
f6a4b1e
Change syntax in fastq-peek.sh
tanyabyte Jul 29, 2024
fae829f
Merge branch 'main' into th-gc-count-dev
tanyabyte Jul 29, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions bin/fastq-peek.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@ LINE_COUNT=$(wc -l < "$FASTQ_FILE")
## Calculate the number of reads (4 lines per read)
READ_COUNT=$((LINE_COUNT / 4))


##Count A, C, T, and G nucleotides in reads
TOTAL_BASE_COUNT=$(grep -o "A\|C\|T\|G" $FASTQ_FILE | wc -l)

Expand All @@ -34,5 +35,6 @@ GC_COUNT=$(grep -o "G\|C" $FASTQ_FILE | wc -l)
##Calculate GC Content of reads (X100 for % of total nts)
GC_CONTENT=$(($GC_COUNT*100/$TOTAL_BASE_COUNT))


echo "Number of reads in $FASTQ_FILE: $READ_COUNT"
echo "GC Content of reads in $FASTQ_FILE: $GC_CONTENT%"
Loading