I'm new to this, so excuse me if it's a stupid mistake I'm making. What I'm really after is expression values for each transcript in a wild-type HEK 293.
I have found SRS211675 in NCBI Sequence Read Archive, downloaded the SRA file, and converted it to .fastq with fastq-dump.
Then I have build the bowtie index of the human transcriptome with:
bowtie-build Homo_sapiens.NCBI36.54.cdna.all.fa homo_sapiens
Then run bowtie:
bowtie -p 4 --sam --best homo_sapiens SRR248532.fastq aligned.sam
I get about 50 'skipped read' warnings and the summary is:
# reads processed: 20954439
# reads with at least one reported alignment: 862675 (4.12%)
# reads that failed to align: 20091764 (95.88%)
Reported 862675 alignments to 1 output stream(s)
It seems that cannot be normal. Where am I going wrong here?
I have found SRS211675 in NCBI Sequence Read Archive, downloaded the SRA file, and converted it to .fastq with fastq-dump.
Then I have build the bowtie index of the human transcriptome with:
bowtie-build Homo_sapiens.NCBI36.54.cdna.all.fa homo_sapiens
Then run bowtie:
bowtie -p 4 --sam --best homo_sapiens SRR248532.fastq aligned.sam
I get about 50 'skipped read' warnings and the summary is:
# reads processed: 20954439
# reads with at least one reported alignment: 862675 (4.12%)
# reads that failed to align: 20091764 (95.88%)
Reported 862675 alignments to 1 output stream(s)
It seems that cannot be normal. Where am I going wrong here?