- download gmap and install cd ~/software
wget http://research-pub.gene.com/gmap/src/gmap-gsnap-2023-07-20.tar.gz
tar xvzf gmap-gsnap-2023-07-20.tar.gz
cd ~/software/gmap-gsnap-2023-07-20
./configure --prefix=$HOME/jcbu/software/gmap
make -j 20
make check
make install
- build gmap index
cd /home/jcbu/refGenome/gencode/mouse/GRCm38.p6_releaseM20/Sequence/gmapIndex
nohup /home/jcbu/jcbu/software/gmap/bin/gmap_build -d GRCm38.gmap -D
/home/jcbu/refGenome/gencode/mouse/GRCm38.p6_releaseM20/Sequence/gmapIndex \
/home/jcbu/refGenome/gencode/mouse/GRCm38.p6_releaseM20/Sequence/WholeGenomeFasta/GRCm38.p6.genome.fa &
3.alignPacBio.py
cd /home/jcbu/YJ/PAIsoseq/ES/TAPIS/gmap/
nohup /usr/bin/python2 /home/jcbu/YJ/PAIsoseq/comp_bio-tapis-44cc05ebc78c/scripts/alignPacBio.m.py \
-p 20 -o Gm_Ctrl_rep1.alignPacBio \
/home/jcbu/refGenome/gencode/mouse/GRCm38.p6_releaseM20/Sequence/gmapIndex/GRCm38.gmap \
GRCm38.gmap \
/home/jcbu/refGenome/gencode/mouse/GRCm38.p6_releaseM20/Sequence/WholeGenomeFasta/GRCm38.p6.genome.fa \
/home/jcbu/YJ/PAIsoseq/ES/ccs/Gm_Ctrl_rep1.bc1001.rmAmbiguous.fasta \
Gm_Ctrl_rep1.alignPacBio.log &
4.run_tapis.py
cd /home/jcbu/YJ/PAIsoseq/ES/TAPIS/gmap/
nohup /usr/bin/python2 /home/jcbu/YJ/PAIsoseq/comp_bio-tapis-44cc05ebc78c/scripts/run_tapis.py \
-s 5 \
-p \
-o /home/jcbu/YJ/PAIsoseq/ES/TAPIS/gmap/Gm_Ctrl_rep1.tapis_out \
/home/jcbu/refGenome/gencode/mouse/GRCm38.p6_releaseM20/Annotation/gencode.vM20.annotation.gtf \
/home/jcbu/YJ/PAIsoseq/ES/TAPIS/gmap/Gm_Ctrl_rep1.alignPacBio/aligned.bam \
Gm_Ctrl_rep1.tapis_out.log &
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Appreciate the contribution but in its current state it's barely useful. Please put formatting. Make an introduction sentence. Explain what the commands are and why you use them. Make it generic. No machine-specific paths and thread/core values. Never use nohup productively.