User: bioinfo

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bioinfo10
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Posts by bioinfo

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Comment: C: How to determine the total average insert size from differently divided from one
... Oh, thanks a lot. But my fastq files are not overlap between reads because read length is shorter than inner distance. So in my case, what is the best option for bbmap? Is it right to calculate after merging the three chromosomses fasta file? ...
written 19 months ago by bioinfo10
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How to determine the total average insert size from differently divided from one fastq data pool to each reference?
... Hi, I have difficulty in calculation for average insert size and standard deviation of RNA-seq NGS data to submit GEO database. I generated two fastq files of paired end read(Read1, Read2) using illumina NGS sequencer. And, I used bacteria genome as reference which has 3 chromosomes. For analysis, ...
calculation size rna-seq written 19 months ago by bioinfo10 • updated 19 months ago by genomax80k
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Comment: C: How to generate GFF3 format that I want?
... And Does it work all of the lines? I mean that example is just simple example. The file I have contains thousands of lines. And I want to make one additional line not change CDS->gene ...
written 22 months ago by bioinfo10
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Comment: C: How to generate GFF3 format that I want?
... I'm doing RNAseq using Tuxedo pipeline. Output data from 'Cuffdiff' doesn't have gene name just ' - ' like this. When I did Cuffdiff using reference with two lines per each gene, it works well and I could see gene name. ...
written 22 months ago by bioinfo10
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Comment: C: How to generate GFF3 format that I want?
... If I have 9 columns and "CDS" containing at column $3, so awk function will be changed awk '$3 == "CDS" {OFS="\t"; print $1,$2,"gene",$4,$5,$6,$7,$8,$9}' original.file >> original.file like this? ...
written 22 months ago by bioinfo10
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Comment: C: How to generate GFF3 format that I want?
... Actually, I'm beginner in using programming.. I'm trying to .. ...
written 22 months ago by bioinfo10
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Comment: C: How to generate GFF3 format that I want?
... Yes I know that GFF3 is 9 columns. I just want to emphasize about the difference of line, not columns. Do you know how to generate like that format I have Ex) Seq_ID FIG CDS 2236 3102 . + 1 gene product But I want to generate the reference like this format Ex) Seq_ID . gene 2236 3102 . + ...
written 22 months ago by bioinfo10
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How to generate GFF3 format that I want?
... Hi I'm trying to analyze bacterial RNA-seq data. To conduct RNAseq, I have annotated file format(gff3) described below Modified gff3 format I have is like this: Sequence_Name . CDS StartPosition EndPosition But I want to generate gff3 format like this: Sequence_Name . ...
sequence rna-seq written 22 months ago by bioinfo10
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How to do Resequencing?
... I am currently doing bacterial resequencing using breseq, but I would like to check for an 'unassigned junction' by sanger sequencing and modify from .gd format command. Where can I change it manually? And is there a site that is easy to use for breseq and other bioinformatics tool? Thank you in ...
resequencing breseq sequencing written 2.2 years ago by bioinfo10
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Comment: C: Cuffmerge error(?) for RNA-seq
... Ohhh.. I'm getting data using cuffmerge!!!!!!! Thank you so much! I had wasted time solving this... Now I solved!! Thank you! ...
written 2.2 years ago by bioinfo10

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