Dailu Guan
Dailu Guan
Can you add the chicken new genome assembly (http://ftp.ensembl.org/pub/release-107/fasta/gallus_gallus/ and ) to browser? The previous assembly (galgal6) supported by the browser missed many chromosomes, but the new one includes all...
I try to install sniffles2 using different strategies, but all failed: 1. pip install sniffles, see error: WARNING: pip is being invoked by an old script wrapper. This will fail...
Recently I found parallel-fastq-dump is not working. I install the recent version from the conda.
Using kit: PCS109 Configurations to consider: "+:SSP,-VNP|-:VNP,-SSP" Traceback (most recent call last): File "/group/zhougrp/dguan/nanopore_annotation/Chicken/.snakemake/conda/ec1f5938/bin/cdna_classifier.py", line 336, in nr_records = utils.count_fastq_records(args.input_fastx) File "/group/zhougrp/dguan/nanopore_annotation/Chicken/.snakemake/conda/ec1f5938/lib/python3.6/site-packages/pychopper/utils.py", line 57, in count_fastq_records b = fh.read(size) File...
My bwa command: bwa-mem2 mem -M -t 24 -p -R '@RG\tID:SAMN10471711\tSM:SAMN10471711\tLB:SAMN10471711\tPL:ILLUMINA' /group/zhougrp/zhoulab/GENOMES/Chicken/EMBL/version107/GRCg7b/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.dna_sm.toplevel.chr.fa 04_trimmed_reads/SAMN10471711_val_1.fq.gz 04_trimmed_reads/SAMN10471711_val_2.fq.gz | samtools view -bS - > 05_aligned_reads/SAMN10471711.aligned.bam MarkDuplicates command: gatk --java-options "-Xmx24G -XX:ParallelGCThreads=12 -Djava.io.tmpdir=Temp" MarkDuplicates -I...
Can use this software in non-human species, e.g. cattle? If yes, how I can build pre-trained model? If human model can be extended to other species?
I am wondering if the software can be used in nonhuman species? If not, can we train a model for other species? Many thanks!
I am wondering when you are planning to update the versions to the latest Python and Pytorch?
Whether the softeare can be extended non-human species, e.g. chicken?
Command: python -u ./selene/selene_sdk/cli.py train.yml --lr=0.1 Error information: Traceback (most recent call last): File "train.py", line 11, in parse_configs_and_run(configs, lr=0.01) File "/home/user/.conda/envs/selene_sdk/lib/python3.7/site-packages/selene_sdk/utils/config_utils.py", line 344, in parse_configs_and_run execute(operations, configs, current_run_output_dir) File...