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

Updated two commands #1

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Updated two commands #1

Changes from all commits
Commits
Show all changes
1 commit
Select commit
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
6 changes: 2 additions & 4 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -101,12 +101,10 @@ fold -w 60 file
```bash
awk '/^>/ {if (seqlen){print seqlen}; print ;seqlen=0;next; } { seqlen = seqlen +length($0)}END{print seqlen}' file.fa
```
#### Reproducible subsampling of a FASTQ file. srand() is the seed for the random number generator - keeps the subsampling the same when the script is run multiple times. 0.01 is the % of reads to output.
#### Subsampling first 100 lines of a FASTQ file using head to subset large data sets.

```bash
cat file.fq | paste - - - - | awk 'BEGIN{srand(1234)}{if(rand() < 0.01) print $0}' | tr '\t' '\n' > out.fq
# If the FASTQ file is gzipped and you want to produce a gizzped output.
zcat file.fq.gz | paste - - - - | awk 'BEGIN{srand(1234)}{if(rand() < 0.01) print $0}' | tr '\t' '\n' > out.fq | gzip out.fq
head --lines=100 file.fq > out.fq
```

#### or look at the Hengli's Seqtk
Expand Down