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dincarnato / RNAFramework

RNA structure probing and post-transcriptional modifications mapping high-throughput data analysis
http://www.rnaframework.com
GNU General Public License v3.0
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rf-count "File contains unsupported line endings ("\r")" #55

Closed jsromanowski closed 3 months ago

jsromanowski commented 6 months ago

Hello,

I am currently trying to use the rf-count command to analyze SNP and indel data from a sorted .bam DNA file (I am assuming this program works for both RNA and DNA files). I downloaded RNAFramework and brough the directory to PATH.

I then ran the following command:

$ rf-count -f NHEJAssayDshortref.fas -orc -m D2_NHEJ_FLsorted.bam

Here, NHEJAssayDshortref.fas is my reference file and D2_NHEJ_FLsorted.bam is my input .bam file I would like analyzed.

I received the following output:

**[+] Making output directory... [+] Guessing file types:

Sample Type 5'-end trimming

D2_NHEJ_FLsorted BAM Ignored

[+] Getting transcripts from reference, and building count table base structure... [!] Exception [Data::IO::Sequence->new()]: File contains unsupported line endings ("\r") -> Caught at /mnt/c/users/josep/Downloads/RNAFramework/lib/Core/Base.pm line 126.**

I am not entirely sure what the unsupported line ending error message is referring to. Is this error because I am using a DNA .bam input rather than RNA .bam? Any help is appreciated. Thanks

dincarnato commented 6 months ago

Hi,

The issue relates to your FASTA file, which was most likely generated using a Windows text editor. You should make sure your file has only "\n" line endings. This can be done on Linux via the dos2unix program.

Best, Danny