kishor2019

Error_report

2

From last few days i am trying to use NextPolish. When i meet the trouble for the first time i went to user guideline and found that the author has...

Hi, I am using trimal v1.4.rev15 to trim and back-translate into codon to make the alignment suitable fo PAML. Since running it i have found that -automated1, -backtrans, -nogaps can...

Generating .hic file with convert.sh

4

I have loaded juicer_tools_1.22.01.jar to the JUICER_JAR variable like as following: JUICER_JAR=/mnt/genome3/Lab_Users/Kishor/DISK_2/softwares/SALSA-master/juicer_tools_1.22.01.jar and i run the program like convert.sh scaffolds #here, scaffolds is the directory where the final fasta, agp...

Hi, I am trying to predict transmembrane protein using tmhmm-2.0c. I have changed the path of perl like as following. First i check the location of perl which perl /usr/bin/perl...

[main_samview] fail to read the header from "-"

1

Bash script: #Set input and parameters round=2 threads=20 read1=/mnt/disk2/Lab_Users/KISHOR/mnspt4/tenili_reseq_50x/X101SC23121795-Z01-J001/00.CleanData/3157_3/3157_3_1.clean.fq.gz read2=/mnt/disk2/Lab_Users/KISHOR/mnspt4/tenili_reseq_50x/X101SC23121795-Z01-J001/00.CleanData/3157_3/3157_3_2.clean.fq.gz input=/mnt/disk2/Lab_Users/KISHOR/mnspt4/assembly_annotation/NECAT/manual/tenili.fa for ((i=1; i tenili.polishtemp.fa; input=tenili.polishtemp.fa; #step2: #index genome file and do alignment bwa index ${input}; bwa mem -t ${threads}...

Hi, I am using gffread to extract protein and cds. In header, i am getting, >rna-XM_063194457.1 the header i need, >rna-XM_063194457.1 gene=LOC134445371 My cmdline: gffread SarPil.gff -g SarPil.fa -x SarPil-cds.fa...

Hi, I am experiencing issues during the scaffolding procedure after genome assembly using finalFusion from SOAPdenovo-r242, as recommended in the manual. I have utilized the following cmds: #for preparing /home/software/SOAPdenovo2/fusion/finalFusion...