bedparse convert fails on nanocompore bed file about bedparse HOT 3 CLOSED

Hi Samir,
based on the error message ("The chromosome of transcript ENST00000368723.4_ACCTC (chr1)") your BED file contains chromosome names in the format "chrN". This is already the UCSC format (whereas Ensembl uses only the chromosomes number without "chr"), so there should be no need to do the conversion..
Just to be sure, you could post the first few lines of the BED file?

from bedparse.

Thanks, I had assumed it was in the ensembl format.
these are the first few lines of the BED file

chr1 153457946 153457951 ENST00000368723.4_ACCTC 2.23094631245163 -
chr1 8862913 8862918 ENST00000234590.10_GAGCG 2.992140476625321 -
chr1 8861355 8861360 ENST00000234590.10_AGCTG 2.9953364808678695 -
chr1 153991134 153991139 ENST00000651669.1_TCCCT 2.856383270637805 +
chr1 153360815 153360820 ENST00000368738.4_GCCTC 4.2618168289065235 +
chr2 84906599 84906604 ENST00000233143.6_TCTCC 2.8439782562306046 +
chr6 31839648 31839653 ENST00000375638.7_ATGCC 2.391610325417182 +

from bedparse.

Hi @samir-watson,
yes, this is UCSC format. You should be able to load it on the Genome Browser as it is.

best
tom

from bedparse.