So, I downloaded sra and then converted to fastq from this link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE99671
I have tried salmon and bwa+htseq-count to align and get readcount. Both of the tools are failed to get any result. The salmon result is only 2% mapped and htseq-count cannot even map a single reads to transcript.
My question is, what do you think happen here? Does the sequencing machine affect this? I noticed the platform to sequence is not illumina. The original author use Lifescope to to do the RNA-seq workflow. Anyway to investigate this? I attached Fastqc result
I have tried to use bowtie to index reference genome in colorspace. The command is this:
bowtie-build -C --threads 18 HG38_90.fa hg38_90_idx
I aligned the file with this command:
bowtie --chunkmbs 500 -C -p 18 -S hg38_90_idx -1 fastq/SRR5644749_1.fastq -2 fastq/SRR5644749_2.fastq SRR5644749.sam
And the result is really bad.
# reads processed: 20826355 # reads with at least one reported alignment: 17671 (0.08%) # reads that failed to align: 20808684 (99.92%)
Any suggestion how to align in colorspace?