User: Pin.Bioinf
Pin.Bioinf • 270
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Im a Health Engineer with a Bioinformatics specialization doing epigenetics research.
Posts by Pin.Bioinf
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I came up with this solution that a contributor in this page proposed to calculate the percentage of reference genome covered :
#Determine number of bases at 0 read depth
zero=$(bedtools genomecov -ibam BAM -g hg38.fasta -bga | awk '$4==0 {bpCountZero+=($3-$2)} {print bpCountZero}' | tail ...
written 11 months ago by
Pin.Bioinf • 270
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... As I asked in a similar question that was closed (thought it was different enough to be asked separately), could I determine the transcriptome size by multiplying uniquely mapped reads by read size?
Here is an example of the report
Number of input reads | 57456000
...
written 11 months ago by
Pin.Bioinf • 270
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... Hello,
I mapped my .fastq files against genome and I got the mapping quality reports. I have that 60M - 70M reads were uniquely mapped and that my reads were 100bp in size.
Can I say that **60M * 100bp (6 000 000 000 bp = 6000 Mb)** is the size of the transcriptome in that sample or am I complet ...
written 11 months ago by
Pin.Bioinf • 270
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... I got this:
1891663623, so these are bp? Do these numbers seem reasonable?
What I did:
bedtools genomecov -ibam input.bam -bg | bedtools merge -i - > covered_36.bed
cat covered_36.bed | awk -F'\t' 'BEGIN{SUM=0}{ SUM+=$3-$2 }END{print SUM}'
1891663623 ...
written 12 months ago by
Pin.Bioinf • 270
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... Thank you! could you help me with the command? I am new to this, how do I keep all regions with at least one read and sum up the size of the intervals with bedtools? Here is my idea:
bedtools genomecov -ibam input.bam -bg to get the regions with at least one read, and then how can I calculate tota ...
written 12 months ago by
Pin.Bioinf • 270
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... Hello,
I want to calculate TMB (mutational load), i know it will not be accurate because its RNA-Seq, but what is the target region generally for RNA-Seq? Similar to WES (30Mb)?
We sequenced with 100b length reads.
I need this to divide non synonymous mutations by this region size number.
Thank ...
written 12 months ago by
Pin.Bioinf • 270
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... Hello,
I want to calculate the Tumor mutational burden of my responders and non responders to treatment.
I have many question regarding this matter:
1. Should I calculate a TMB for responders and another TMB for non responders or only a global TMB for all samples?
2. **samtools mpileup , bcftoo ...
written 12 months ago by
Pin.Bioinf • 270
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... Hello, I have a normalized expression matrix that has many genes. I also have clinical data for the same samples of the matrix. Some data is numeric (age, levels of LDL, tumor size...), and some is categorical (sex, response to therapy, subtype of tumour...)
What kind of tests can I use to assess c ...
written 12 months ago by
Pin.Bioinf • 270
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... I would like to build a phylogenetic tree for around 40-50 patients with breast cancer based on SNP and CNAs I was asked for it by a fellow biologist, I am completely new to phylogenetics and I have no clue where to start. Do you have any recommendations on pipelines or brief steps I should follow ...
written 13 months ago by
Pin.Bioinf • 270
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... Yes, I agree. I was using default parameters, which were "complete" and "euclidean". I tried euclidean with ward.D2 and still, the differentiation between tumor and controls is not clear, it is a blur in the middle of both, and some tumors are the same color as controls as in my original heatmap. ...
written 13 months ago by
Pin.Bioinf • 270
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