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Error when running `Mandalorion_just_align.py`

2

I got this error when running the script on the ONT reads from the paper: ``` Traceback (most recent call last): File "Mandalorion_3_Remove_ISPCR_Sequences.py", line 109, in find_ispcr(path+'/'+input1) File "Mandalorion_3_Remove_ISPCR_Sequences.py", line...

kmnip

When running Mandalorion with the following command: python3 Mandalorion_just_align.py -f /data/csijcs/nanopore/WW_Nanopore_K562_107/basecalls/workspace/all/WW_Nanopore_K562_107_all_pass.fastq -g /data/csijcs/nanopore/GRCh38/GRCh38 -q 2 -t 64 I keep getting this issue: Unable to find genome directory /usr/local/share//data/csijcs/nanopore/GRCh38. Either recompile...

ghost

Right now mandalorion uses the geometric mean to calculate a cutoff for read quality, but this leads to artificially inflated mean scores. Albacore reports the arithmetic mean. This may cause...

conchoecia

In using Mandalorion we identified an issue where gene start and end positions were being defined as the last exon present in the .gtf annotation file.

paulranum11

Hi, I was having issues with the script 'Mandalorion_7_Gene_expression.py' ; it was hanging on the read_data function at a specific line and never moving on. I created a script that...

abayega

Dear prof， My name is Huamei Li, and from china. when I read the python code of Mandalorion, many questions have been generated: 1. Mandalorion_3_Remove_ISPCR_Sequences.py: the following shortcut shows ISPCR...

lihuamei

Line number 31: while x

lihuamei

No paths found for XXXX_p_p

9

Hi I have run this command; python3 Mandalorion_just_align.py -f myfile.fastq -g GRCh37 -q 9 And then I got many these message. No paths found for xxxxxxxxxxxxxxxxxx for approximately one third...

satomimitsuhashi

Interpreting output BED files

2

Hi there. I've looked through the Mandalorion documentation here, but I still have a few clarifications regarding interpretation of some of the BED output files. The following snippet is from...

malloryfreeberg

Hi, I would like to use your Mandalorion_demultiplex_and_align.py but I do not know the content of the sample sheet required. Is it like the "content_file_example" you provide in the Mandalorion...

ma-diroma