Stringtie error: Error: input file –e cannot be found!
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11 weeks ago
menyawino • 0

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

RNA-seq tuxedo stringtie transcriptomics • 346 views
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11 weeks ago
Mensur Dlakic ★ 27k

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.

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Oh again copying and pasting from papers that use weird symbols! Thank you so much it worked

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