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getfasta -rna option does not work for plus strand line when setting -s option #1084

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NaotoKubota opened this issue Mar 27, 2024 · 1 comment

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@NaotoKubota
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Hi, I report a possible bug in getfasta.
It seems -rna option does not work for plus strand record when setting -s option.
Here is a test bed file (test.bed):

chr3	89235292	89235302	test	0	+
chr3	89235292	89235302	test	0	-

I ran the command:

bedtools getfasta -fi GRCm38.primary_assembly.genome.fa -bed test.bed -s -rna

the output was here:

>chr3:89235292-89235302(+)
CTGTAGGAGG
>chr3:89235292-89235302(-)
CCUCCUACAG

The T in >chr3:89235292-89235302(+) are supposed to be U.

Could you please take a look into it?
The version of bedtools I used was v2.30.0.

Best,

@HibaLaghrissi
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Hello,
I have the same issue, have you found a solution ?
Thank you

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