daveuu
commented
8 years ago Hi,
This is an excellent feature request. I added an option --prepared to the AlignReads commands allowing you to skip the PrepareReads module and go straight from CollectData to AlignReads. First update BAGA with these commands:
cd baga
git fetch origin
git reset --hard origin/master
cd ..Then a typical work flow could look like this (the last command uses the new --prepared option):
baga/baga_cli.py Dependencies \
--checkgetfor CollectData
baga/baga_cli.py CollectData \
--reads_group_name myreads \
--reads_path reads/*_R[12]_*.fastq.gz # shell expansion pattern to match one or more pairs of reads
baga/baga_cli.py CollectData \
--genomes <chromosome/genome accession number> \
--email <your email address for NCBIs Entrez system>
baga/baga_cli.py Dependencies \
--checkgetfor AlignReads
baga/baga_cli.py AlignReads \
--reads_name myreads \
--genome_name <chromosome/genome accession number as saved by BAGA> \
--prepared \
--alignLet me know if that works for you. I'll add this to the manual that is almost done!
pauruihu
Hello again! What would you recommend to change in order to avoid the trimming step and complete the whole process? I thought about it because my reads are already preprocessed and cleaned. I understand that if I just eliminate that step there may be some outputs not generated that are necessary to continue... Thank you (I'm looking forward to the documentation ;))