Zhang Jingjing
Zhang Jingjing
$ perl vcf2maf.pl --input-vcf xxx.snp.vcf --output-maf test.maf --ref-fasta ../pig.dna.toplevel.fa STATUS: Running VEP and writing to: xxx.snp.vep.vcf ERROR: Cannot find VEP script under: /yyy/miniconda3/bin
Hi, I was wondering how can I deal with this problem? I can't install the Bio::EnsEMBL::Registry package. https://github.com/Ensembl/ensembl-vep/blob/316682594c11101535882b29983e07cd2cb53420/modules/Bio/EnsEMBL/VEP/BaseVEP.pm#L56 `./vep Can't locate Bio/EnsEMBL/Registry.pm in @INC (@INC contains: /xxx/ensembl-vep-release-106/modules /xxx/ensembl-vep-release-106 /xxx/software/mirdeep2-0.1.3/lib/perl5 /home/dell/vep/ensembl-vep...
**What do you want to know?** In my output files, there is no tbl file. command:`time RepeatMasker -parallel 30 -species murinae -html -gff Mus_musculus_c57bl6nj.C57BL_6NJ_v1.dna.toplevel.fa` * Have you installed RepBase RepeatMasker...
## install error log $ pip install misopy Requirement already satisfied: misopy in /Parastor300s_G30S/zhangjj/software/miniconda3/lib/python3.9/site-packages (0.5.4) Requirement already satisfied: scipy>=0.9.0 in /Parastor300s_G30S/zhangjj/software/miniconda3/lib/python3.9/site-packages (from misopy) (1.10.0) Requirement already satisfied: pysam>=0.6.0 in /Parastor300s_G30S/zhangjj/software/miniconda3/lib/python3.9/site-packages...
## INSTALL build]$ make Scanning dependencies of target PanGenieLib [ 1%] Building CXX object src/CMakeFiles/PanGenieLib.dir/emissionprobabilitycomputer.cpp.o [ 2%] Building CXX object src/CMakeFiles/PanGenieLib.dir/copynumber.cpp.o [ 4%] Building CXX object src/CMakeFiles/PanGenieLib.dir/commandlineparser.cpp.o [ 5%] Building...
Hi, why some records are "+" for example: chr1 1391725 chr1:1391725:FG N 162 PASS ABHet=0.5;ABHom=1;AC=1;AF=0.0001139;AN=8776;END=1391725;LEFT_SVINSSEQ=AAAAGTTAAGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAAAAAATTAGCCGGGCGAGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCCAGGGGGCGGAGCCTGCAGTGAGCCGAGATTGCGCCACTGCACTCCAGCCTGGGCGACAGCGAGACTCCGTCTCAAAAAAAA;MaxAAS=9;MaxAASR=0.5;MaxAltPP=9;NHet=1;NHomAlt=0;NHomRef=4387;NUM_MERGED_SVS=1;PASS_AC=1;PASS_AN=8774;PASS_ratio=0.9998;QD=16.2;RELATED_SV_ID=209;RIGHT_SVINSSEQ=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA;RefLen=1;SVMODEL=AGGREGATED;SVTYPE=INS;SV_ID=208;SeqDepth=158115;VarType=FG GT:FT:AD:MD:DP:RA:PP:GQ:PL 0/0:PASS:54,0:1:55:55,1:0:99:0,150,255
minigraph]$ make gcc -g -Wall -Wc++-compat -std=c99 -msse4 -O3 kalloc.o kthread.o algo.o sys.o gfa-base.o gfa-io.o gfa-aug.o gfa-bbl.o gfa-ed.o sketch.o misc.o bseq.o options.o shortk.o miniwfa.o index.o lchain.o gchain1.o galign.o gcmisc.o map-algo.o...
## Command python3 PrepareAA.py -s R18008004LD01-A130017-1 -t 4 --cnvkit_dir /xxxj/software/cnvkit/cnvkit.py --bam R18008004LD01-A130017-1.bam --ref GRCh38 -o R18008004LD01-A130017-1_AA_OUT_10x.expand2.30x --run_AA --run_AC ## Log file Wrote R18008004LD01-A130017-1_AA_OUT_10x.expand2.30x/R18008004LD01-A130017-1_cnvkit_output/R18008004LD01-A130017-1.cns with 382 regions Global ref name is...
##Question A large number of regions are missing without annotations. I have a bed file with 38685 lines, but only less than 9549 lines have been annotated. ##Step step1：read genome...
# command check_strandedness --gtf /xxx/Mus_musculus.GRCm38.102.gtf --transcripts /xxx/Mus_musculus.GRCm38.dna.toplevel.fa SRR1538550.fastq.gz # log usage: check_strandedness [-h] -g GTF [-fa TRANSCRIPTS] [-n NREADS] -r1 READS_1 -r2 READS_2 [-k KALLISTO_INDEX] [-p] check_strandedness: error: the following...