Dr. Manoj Kumar

Hi, I installed prokka and roary using conda. However, when I run the programs, they are showing the following error. Any help will be appreciated to solve the problem. Error:...

IQ-TREE taking so long to generate the results

1

Hi, I have an alignment file generated from snippy. Now I am using IQ-Tree with 480 sequences for constructing phylogenetic tree. I ran IQ-tree with the following command. However, it...

snippy error

2

I am running snippy using following command. However, it shows the following error.. snippy --cpus 8 --outdir variants --ref reference.gbk --R1 trimmed_S_010_R1.fastq.gz --R2 trimmed_S_010_R2.fastq.gz ### snpEff build -c reference/snpeff.config -dataDir...

How to use masking file

5

Hi, I am working to identify hqSNPs using snippy. I used Mummer for masking the repeats in the reference genome. I am trying to understand how to use the output...

[question]

32

I am trying bactopia with only one sample but it is taking so long (around 2-3 hours) and still running. Is there any error in the command? bactopia --R1 bactopia_fastqs/1-Ent_R1.fastq.gz...

Hi, I have a .txt file generated from featureCounts file generated from featureCounts. I want to use DEseq2 for Differential expression analysis. Please suggest any script to run the program....

Not results generating?

4

I am following these commands. However, I am getting blank output file. minimap2/minimap2 -x ava-pb -t8 pb-reads.fq pb-reads.fq | gzip -1 > reads.paf.gz # Layout miniasm/miniasm -f reads.fq reads.paf.gz >...

ERROR: while making index file

1

Hi, I am using the following command to make the index file. However, I am getting an ERROR. ./kallisto index -i /DataAnalysis/kallisto_test/transcripts.idx /DataAnalysis/kallisto_test/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz ERROR: [build] loading fasta file /DataAnalysis/kallisto_test/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz [build]...

How the calculated the decay line by nonlinear regression to the LD plot?

3

Hi, I am trying to add the non-linear regression tendency line to the Linkage Disequilibrium (LD) plot. I followed the manual document of PopLDdecay and got the plot. However, I...

Issue in merging several vcfs

3

Hi, I installed bcftools and I ran bgzip and indexed the files using following commands. bgzip -c file1.vcf > file1.vcf.gz bcftools index file1.vcf.gz However, once I merged using following command,...