User: barrypraveen

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barrypraveen30
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Posts by barrypraveen

<prev • 78 results • page 1 of 8 • next >
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Comment: C: How to calculate per base coverage from the .bam file?
... got it....now its fine ...
written 10 months ago by barrypraveen30
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Comment: C: How to calculate per base coverage from the .bam file?
... actually it is not a gene. it is a snoRNA. Just for saying i wrote as a gene. but when i try samtool depth > samtools depth -b missed_bed.bed -f PC1_Yale_PRS_sorted.bam i got error "Does the file "PC1_Yale_PRS_sorted.bam" really contain a list of files and do all exist?" I really don't know ...
written 10 months ago by barrypraveen30
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Comment: C: How to calculate per base coverage from the .bam file?
... I have to plot that expression. I have RPKM values for that gene but if I plot in the excel file it comes like a point. my idea is like showing the distribution of the expression. lets say x-axis is a length of the gene in the y-axis expression of the gene. ...
written 10 months ago by barrypraveen30
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How to calculate per base coverage from the .bam file?
... Hi all, I have some genes which are expressed in differentially compare to wild type, so i want to calculate perbase coverage from the BAM files. How to calculate that one. ...
R next-gen rna-seq written 10 months ago by barrypraveen30 • updated 10 months ago by ATpoint36k
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how to define more stringent parameters for the snoscan to indentify snoRNA target on rRNA?
... Hi, i have identified some of snoRNA from leishmania. I am interested to identify the targets of those snoRNAs in rRNA. I have 50 snoRNA transcripts when i gave this as an input sequence the **snoscan** software producing huge amount of data. is there any way to optimize the parameters to get good ...
genome sequence rna-seq written 12 months ago by barrypraveen30
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Comment: C: How to extract un annotated (With abundant) small RNA transcript?
... Sorry for the inconvenience, not able to add snippet. But I can explain. I have BAM and certain small RNA BED files with me. I am screening manually by IGV. My question is it possible to identify the unannotated transcript coordinates or something etc? ...
written 19 months ago by barrypraveen30
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How to extract un annotated (With abundant) small RNA transcript?
... Hi, I have sequenced file and known small and non-coding RNA bed files. Is it possible to get unannotated with abundant small RNA transcript from my sequencing file? ...
assembly rna-seq sequencing written 19 months ago by barrypraveen30 • updated 19 months ago by geek_y11k
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multicuv error Could not find indexes
... I am trying to get new coordinated for my sequencing file so i tried to align my new version of the genomic file (TB927_v5.1). I used smalt to get sam file. I converted my sam file into bam file using this command: samtools view -h -b -S out.sam > out.bam Next, i used to multicuv bedt ...
software error alignment rna-seq written 2.1 years ago by barrypraveen30 • updated 2.1 years ago by Nitin Narwade450
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Comment: C: duplicate 'row.names' are not allowed
... I am trying to find some new novel transcript from my sequencing file so i did **multicov** from bed tools to get the read counts. **bedtools multicov -bams DS1.bam DS2.bam -bed transcript_I.bed > all_transcripts_I.tsv** From that i took multicov output as a DESeq2 input file (all_transcripts ...
written 2.2 years ago by barrypraveen30
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Comment: C: duplicate 'row.names' are not allowed
... **R function i Uesd :** countdata <- read.table("file5.tsv", header=TRUE, row.names=1) **The error i got :** Error in read.table("file5.tsv", header = TRUE, row.names = 1) : duplicate 'row.names' are not allowed ...
written 2.2 years ago by barrypraveen30

Latest awards to barrypraveen

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Popular Question 2.1 years ago, created a question with more than 1,000 views. For Difference between single end and paired end library preparation in RNA Sequencing?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For How calculate RPKM values for DESeq?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Difference between single end and paired end library preparation in RNA Sequencing?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For How calculate RPKM values for DESeq?
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