barbarian

About

Username
barbarian
Location
Japan
Joined
Visits
20
Last Active
Roles
Member
Points
27
Badges
5
Location
Japan
Full Name
Bharata Kalbuaji

Comments

  • (Quote) My end goal is to get variation. I have tried samtools+bcftools to call variation. The output of bcftools is vcf file and that is what I want. It is pretty basic actually. I just want to ask whether BAM which come from RNA-seq experiments ca…
  • (Quote) I want to do variant calling but I have read somewhere before in GATK, the exome seq coverage is small compare to RNA-seq so data from exome-seq is not good for variant calling. That's why I tried to do variant calling using RNA-seq. So, is …
  • @Sheila I noticed that there is no Hg38 data in the bundle. I mapped my data using Hg38 as reference. For 1000G snp, I get the phase 3 from Ensemble FTP which is suitable for Hg38. Can you suggest any other place to download the data set which can …
  • What kind of sequencing data type is good for MuTect input? RNA-seq or Exome-seq?
  • (Quote) Yah you are right. Actually I feel that it is just impossible to detect SNP in the promoter regions with such low coverage. So, I just tried to finish my analysis process so that at least I can get SNP in the exon region which is has good co…
  • (Quote) Hello, Thank you for your reply. I don't think this is caused by low base quality because in the data, reads in exon regions have quite good quailty but it also removed in the bamout file. Compare to the input, which is bam file after BaseR…
  • My normal work flow is the one without intervals. The step I tried using interval because I don't understand the parameter -L from the sample. It said in the CommandLineGATK guide L is like this: One or more genomic intervals over which to operate S…
  • This is my command after I aligned, deduped, and sorted 1. NCigar java -jar /opt/GATK/GenomeAnalysisTK.jar -T SplitNCigarReads -R ../../EnsembleHG38/primary.fa -I SRR1656634.dedup.grouped.ordered.bam -o 34.splitted.bam -rf ReassignOneMappingQuality…
  • Hello, Thank you for your suggestion. I thought the workflow is the same and I skipped that part. I have done the N cigars step and redone the data processing,but it still the same. The screenshot is here: https://dropbox.com/s/hhigaezmo6kdgzd/scr…
  • Hello Mrs. Geraldine, So, I have checked the alignment for both RNA-seq and Exome-seq (same sample) and I noticed that the coverage outside exon in Exome-seq is almost 0 but I could find a little coverage (beween 0-20 reads) in RNA-seq data. I deci…