User: barrypraveen

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barrypraveen10
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1 year, 11 months ago
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Posts by barrypraveen

<prev • 73 results • page 1 of 8 • next >
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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 8 days ago by barrypraveen10
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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 8 days ago by barrypraveen10 • updated 8 days ago by geek_y8.8k
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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 6 months ago by barrypraveen10 • updated 6 months ago by Nitin Narwade340
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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 7 months ago by barrypraveen10
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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 7 months ago by barrypraveen10
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duplicate 'row.names' are not allowed
... I have RNA-SEQ data i wanted to do DESeq (DEseq2 i am using). When i try to open my file it shows **duplicate 'row.names' are not allowed** like that. I already have gone through all kinds of possible ways which were discussed before but nothing worked. **This is my data** Tb927_01_v5.1 5 ...
software error R rna-seq written 7 months ago by barrypraveen10 • updated 10 days ago by paul.boisseaux0
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Comment: C: how to find new transcript from bam file?
... it's very hard to say because we prepared the samples in a different way. it reduces the rRNAs from 80% to 20% and my snoRNAs are enriched from 5% to 30%. ...
written 7 months ago by barrypraveen10
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Comment: C: memory is low reading termination?
... how many BAM files we can load. Because i have many. ...
written 7 months ago by barrypraveen10
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Comment: C: memory is low reading termination?
... Ok thanks, previously i allocated more RAM for IGV but it did not any better results. ...
written 7 months ago by barrypraveen10
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memory is low reading termination?
... I have lots of BAM file. I am looking novel transcripts from my bam file by using IGV. I have 4gb (Linux) and 8 GB Windows 10 systems. I want to allocate more RAM memory for IGV help me how to proceed. ...
alignment next-gen rna-seq written 7 months ago by barrypraveen10 • updated 7 months ago by genomax60k

Latest awards to barrypraveen

Popular Question 6 months 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 6 months ago, created a question with more than 1,000 views. For How calculate RPKM values for DESeq?
Popular Question 14 months 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 14 months ago, created a question with more than 1,000 views. For How calculate RPKM values for DESeq?
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