Obtaining SRRIDs in SRA accession table from GSMID
grep ^SRR SRA_Accessions.tab | grep GSM1379814
Shell scripts for data handling Another simple way is to check the SRR ID of your sample in SRA Run Browser: http://trace.ncbi.nlm.nih.gov/Traces/sra/ "Browse" -> "Run Browser" -> then input your ID The LAYOUT result will tell you. Also, the 'Reads' label shows 1 read for single end, and 2 reads for paired end.
Syncing data from local to remote
rsync -avzh --progress Methylation_epic/user@xyz.com:/work/users/abc/SINGLECELL/Raw-data/ SYncing data from REMOTE to REMOTE
rsync -vuar --progress BwFormat.zip user@uio.no:/storage/scratch/ftp/Folder1/folder1_1
shell scripts:
BAMtoBW-treatment : bamCoverage command of deeptools for converting BAM files to BW
Changing Timestamps : It changes time stamps of the files.
REMOVING-DUPLICATE ID : removing duplicate id´s
Single_End_BAMTOBW : bamCoverage command of deeptools for converting BAM files to BW
bamToBW : bamCoverage command of deeptools for converting BAM files to BW
bwtobedconversion_liftover - bedops tools bigwid to bed and wig to bedformat