How should I align my single-end fastq file?

How should I align my single-end fastq file?

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I have this RNA-seq fastq file which is SINGLE-end.

However, I couldn’t figure out these fastq files are unstranded or strand-specific.

I cannot even know if their orientation is forward or reversed…

I ran STAR alignment with command:

STAR --runThreadN 32 --genomeDir [ENSEMBL reference folder] 
--readFilesIn [fastq file name] --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts 
--outFileNamePrefix [output file name]

but when I convert the result to cpm and compare it to paper’s cpm matrix, it’s quite different.

What should I do?


RNAseq


raw-count


fastq

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