I'm new to RNA-seq. I keep getting an error from stringtie when I try to perform differential expression with -e option.
Here's a full command for one sample:
> stringtie \
–e \
–B \
-p 8 \
-G /mnt/Partition_2/Interns/Omar_Ahmed/03_assembly/merged/stringtie_merged.gtf \
-o /mnt/Partition_2/Interns/Omar_Ahmed/04_dea/healthy/SRR24302638/SRR24302638.gtf \
/mnt/Partition_2/Interns/Omar_Ahmed/02_alignment/hisat2/healthy/SRR24302638/SRR24302638.bam
This gives this error
Error: input file –e cannot be found!
I checked the file paths and even moved everything to one folder and nothing helps. TIA
To my eye it appears that you are typing or pasting incorrect dash symbols for –e and –B. Compare that with what you are typing for -p and -G. I will put them next to each other so you can see: –e -p. Hopefully you can see that next to e you have a longer dash. I suspect it will be fixed when you use the same dash for the first two switches as for the rest.
Oh again copying and pasting from papers that use weird symbols! Thank you so much it worked
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