Could someone please explain to me how am I supposed to do the following steps?
" *(1) downloaded the files SRR030222.sra, SRR030223.sra, SRR030224.sra and SRR030225.sra containing the unmapped short reads for two replicates of from the DICERex5 sample and two replicates from the HCT116 sample respectively. Converted them to FASTQ-formatted files using the NCBI SRA Toolkit.
(2) produced SAM-formatted files by mapping the short reads to the reference human genome (NCBI Build 37.5) using the Bowtie [2] algorithm. Only uniquely mapped reads are reported.
(3) compressed the SAM formatted files to BAM and ordered them by reference name first, then by genomic position by using SAMtools [3].* "
For part 1 I downloaded to files using the FTP site and I used to file fastq-dump.exe to find the fastq format. After that I have no idea what to do. Help is appreciated. Wish Matlab documentation was more descriptive though.
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