A)
grep '^@' test.fastq |wc -l (or) wc -l test.fastq (and then divide by 4)
B)
cp /corral-repl/utexas/BioITeam/rnaseq_course/C .
C)
grep 'ACTACCGATCCA' test.fastq |wc -l
D)
module load fastx_toolkit
fastx_clipper -a ACTACCGATCCA -i test.fastq -o <outputfile> -l <discardSeqsShorterThanN>
E) module load cufflinks
nano commands.cufflinks
cufflinks -p 2 -g genes.formatted.gtf -o <output> test.bam
module load python
launcher_creator.py -n cufflinks -t 01:00:00 -j commands.cufflinks -q development -a CCBB
qsub launcher_creator.py
F) samtools view test.bam 2L:7620-7700
G) scp + open in IGV
Further...
H) sed 's/,/ /g' DESeq_output.csv |awk '{if ((($7>=1)||($7<=1))&&($8<=0.05)) print $2}'|wc -l
