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arq5x / bedtools2

bedtools - the swiss army knife for genome arithmetic
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getfasta -rna option does not work for plus strand line when setting -s option #1084

Open NaotoKubota opened 8 months ago

NaotoKubota commented 8 months ago

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 commented 4 months ago

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