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• STAR RNA - Generate Wiggle Plots from already aligned BAM files
  Hi All, Is it possible to re-run STAR RNA aligner to obtain wiggle plots on already aligned and ...
• Question : Plotting Per Chromosome/All Chromosome Coverage From Ngs Bam File
  Hi, I wish to plot per chromosome coverage from a BAM file obtained from aligning exome sequenci...
• getting a list of alignment with a particular bam tag from a bam file
  I have a list of values for a bam tag called XC (say needed.txt). I would like to extract the ali...
• Alignment plot of a small extract (sequence) from a .bam file
  Hi I have a made variant callings of a bam file. Now instead of checking 100 variants one by one...
• Tool/scripts for quantifying proportion of aligned RNA-seq reads on the basis of their types ?
  I'm working with RNA-seq data and I'm already done with alignment(i.e. I have the BAM files). My ...
• How To Plot Rarefaction/Saturation Curve Based On Bam File Generated By Tophat?
  I want to determine whether the sequencing depth is enough to cover most of the transcripts in th...
• createRepeatLandscape in RepeatMasker
  I have used the calcDivergenceFromAlign.pl script available in the RepeatMasker package, to produ...
• Spliced alignment information from bam file
  How do I know if an alignment is spliced by looking at SAM format? I need to find spliced alignme...
• Estimating Insert Size From Paired End Data.
  Hi, I have paired end data from illumina. To estimate the insert size in silico ( from scratch )...
• Quick and easy way to get alignment stats from many SAM/BAM files?
  Is there a good tool for extracting basic alignment stats from multiple BAMs/SAMs? I have tried `...
• bimodal distribution of bam mapping quality
  I have some RNA-Seq data that I analyzed with tophat2. The command that I used to generate it is...
• Can I open a BAM file without a header in Rsamtools?
  Dear all, I am trying to analyse the quality of reads from a BAM file but the BAM file does not ...
• good CIGAR value but poor MAPQ value
  I was a bit confused by the output of a bwa read-alignment. I have observations that return a goo...
• Is there a tools to select alignment from BAM files with particular tag value?
  I'm interested in selecting only uniquely mapped reads from Hisat2 alignment bam files. I think I...
• MNase-seq / fragment size selection
  Hello guys I have an MNase-seq bam file (~400 million reads) that I'm trying to split into two d...
• Get Reference file from BAM
  Is is possible to determine the reference file from a BAM file? I want to programatically determi...
• Plot reads from .BAM file above reference sequence in R?
  I want to plot something like this: ![enter image description here][1] This was produced with G...
• Circos Histogram Bam File
  I've a BAM that I'd like to show its coverage off in a circos plot (http://circos.ca/documentatio...
• [CNV] doubt with the results of cn.mops on different reference genomes
  Hello everyone! I am working with DNA-seq and the cn.mops R package. Firstly, i was working with...
• chipseq data normalization
  I have 4 chipseq data (Bam files) files from Input, control treated and knockout of a gene. Now w...
• How to count positively and negatively aligned reads in a bam file?
  I have a bam file and I would like to count the number of plus and minus strand aligned tothe ref...
• Read File Format .Bam
  My research is related to the manufacture of snp database. constraints that occurs is how to rea...