Comments (5)
Hi,
In case of alignment files such as BAM format you do not need to add [-ref] as a parameter, this will be only to proceed to align raw reads (FastQ format) to the reference human genome.
You should just exclude the -ref as the following:
python Yleaf.py -bam file.bam -pos Position_files/hg38.txt -out out -r 1 -q 20 -b 90 -t 1
Hope this helps!
Best,
Diego
from yleaf.
it did.
Thank you Diego =)
from yleaf.
Hi, I get the same error but within FASTQ files as well. I ran the command like in the example mentioned in the README.
python Yleaf.py -fastq S19_19.fastq -out out -r 1 -q 20 -b 90 -t 16 -ref hg38
I receive the same error message as mentioned above. Am I doing anything obviously incorrect?
Carl
from yleaf.
Hi,
Sure! When running Yleaf with FASTQ files you first need to create an indexed file with BWA. This is included by running "python install.py". Then, Select the genome build, in your case hg38. This might take a while depending on your network and CPU to download and generate the index reference genome.
Lastly, for running Yleaf you can do something like:
python Yleaf.py -fastq S19_19.fastq -out out -r 1 -q 20 -b 90 -t 16 -pos Position_files/hg38.txt -f hg38/hg38.fasta
Hope this helps!
Best,
Diego
from yleaf.
from yleaf.
Related Issues (15)
- No such file or directory: 'Hg_Prediction_tables/tree.json' HOT 7
- hg19 HOT 7
- What if input paired-end reads fastq file HOT 2
- Error indicated when running Yleaf installed with conda on CentOs HOT 1
- Few queries HOT 2
- Old Prediction Option not using the correct files HOT 2
- output HOT 1
- Updating position files HOT 2
- Difference in results between Yleaf v3.0.1 and v3.1 (master) HOT 15
- 2.3 release HOT 2
- Article link in the readme is broken HOT 1
- No haplogroup result if I use the -r1 option
- How to choose the position files? HOT 2
- Docs: mention the support of alignment.bam.bai only, not alignment.bai HOT 1
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