Bioinformatics Questions, Problems & Solutions : TransWikia.com ~ Page 20

Parsing .vcf file for this information

I have a .vcf file https://www.dropbox.com/s/8v73nppwg3a1tnd/LP2000109-DNA_A01_vs_LP2000103-DNA_A01.SVannotated.txt?dl=0 with this header##startTime=Fri Mar 29 16:46:32 2019#CHROM POS ID REF ALT QUAL FILTER INFO...

Asked on 06/17/2021

2 answer

Is there an efficient way to extract CIGAR strings for read pairs from bam files with python?

I am working with bam files and I have to check if reads of a specific position or their mates are soft clipped. So, I am looking for a fast...

Asked on 06/16/2021 by Mereven

1 answer

Filtering genes from cuffdiff results

This question has also been asked on Biostars I have run cuffdiff (with statistics turned ON) to compare two groups of samples: Control group and Late AD...

Asked on 06/13/2021 by sujaypatil

1 answer

Low Fraction of usable antibody reads in CiteSeq

we performed a combined gene expression and CiteSeq experiment with the 10x VDJ kit and 20 conjugated antibodies and sequenced on hiseq. I used cellranger to process the sequencing output....

Asked on 06/12/2021 by gypti

1 answer

RNA_Seq Analysis in R, propmapped function issue

I'm currently trying to learn RNA-seq data analysis and differential expression in R. I've been using the Combine lab tutorial. Everything was running well until the tutorial...

Asked on 06/11/2021 by PA_Lvl

1 answer

Selecting part of an extracted ligand

I have the PDB 6LU7.I extracted the ligand using extract lig, org and then the protein using extract prot, poly. The ligand has three parts:...

Asked on 06/11/2021 by user8338

1 answer

Proper use of BWA MEM on multiplexed GBS sample

I have a multiplexed lane of GBS sequencing reads as a fastq file. I understand the first step is to demultiplex and trim the adapter sequences from the reads. This...

Asked on 06/10/2021 by PlantGeek519

2 answer

co-occurrence analysis and visualization for amplicon microbial data

I am trying to learn co-occurrence analysis for microbial data. I got relative abundance at the genera level for 50 genera in 19 samples. I understand that for network analysis...

Asked on 06/09/2021

0 answer

How do I create a VCF file of all known pathogenic mutations in a gene of interest?

I would like to create a list (probably .vcf format would be good) of all known pathogenic missense mutations in a human gene of interest and then add other variants...

Asked on 06/08/2021 by Nereus

1 answer

How do I write tests for a snakemake pipeline?

I've been playing with snakemake, which is really powerful, however, I'd like to create a 'unit test' for the whole pipeline. e.g. a way to call the pipeline that tests...

Asked on 06/08/2021

2 answer

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