Answers

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