#Useful scripts Downloadsra is to download SRA data by SRR ID in batch

##Add miRNA2target data and script miRNA2target.dict.picke and target2miRNA.dict.pickle are the comprehensive miRNA target data we collected from main miRNA database with experimently validated or predicted target. We can use find.py to find corresponding target.

##Add get_sequence_by_mir_name.py Use Bio.SeqIO to extract miRNA sequence from mature.fa downloaded from miRBase.
It's stupid that it doesn't use regular expression but extact to match miRNA ID. The result file will named input_miRNA_ID_list.fasta.

##Add findMotifByHand.py Find motif by hand.

##Add Han Server New server address

##Add sortChromosomeAndPosition.py Sort human vcf, bed, gff, gtf files in chromsome order.

Add mapFileUUID2submitterID.py

Map GDC data uuid to submitter ID through the GDC-API. Input file is manifest downloaded from GDC-Portal

Add gdc_download.sh

Download gdc data in 20 parallel, and check md5. The gdc token is not provided. You should speciy the gdc tokens.

Add generalParallel

Simple script for running scripts in parallel, The input file is your bash repeative commands, default parallel is 20.

Add extractOriginalBam2RegionalBam2.sh

It's used for extract bam based on the bed by samtools. And, also it's a simple tamplate for handling many bam files in parallel.