User: EVR

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EVR530
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Posts by EVR

<prev • 169 results • page 1 of 17 • next >
3
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Identifying miRNA, RNA-binding sites in UTRs
... HI all, I have UTRs regions of many transcripts of a non-model organism of my interest and I would like to identify the miRNA, RNA binding sites and post transcriptional regulatory elements in the UTRs. Can you suggest a database where can I download the target sequences. Thanks in advance ...
minra rna-binding protein utrs written 18 months ago by EVR530 • updated 18 months ago by Russ450
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3
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Answer: A: Visualization of Gene Ontology using bubble plot.
... HI Agamy89, I generally use [REVIGO][1] for visualizing the GOs. The best part of revigo is that all its plots are generated in R and you can download the R script and work on it to suit your needs [1]: http://revigo.irb.hr/ ...
written 18 months ago by EVR530
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Comment: C: Merging bed intervals within a group
... Hi, Thanks for your reply. I tried your code, it gave the following output 11561749 14491295 ...
written 21 months ago by EVR530
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Merging bed intervals within a group
... Hi, I have a bed file like following: PGRP-SA-PA 11561749 11561803 PGRP-SA-PA 11561806 11561873 PGRP-SA-PA 11561875 11561925 noc-PB 14490900 14490989 noc-PB 14491004 14491065 noc-PB 14491076 14491106 noc-PB 14491117 14491182 noc-PB 14491201 14491295 I would like to ...
bedtools bed bedops written 21 months ago by EVR530
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7 follow
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Average intron length in Drosophila melagnoster
... Hi All, What is average or median intron length in Drosophila melagnoster genome. Is it 65 nts long? kindly guide me Thanks in advance. ...
drosophila intron_length written 21 months ago by EVR530 • updated 21 months ago by Malcolm.Cook1.0k
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Comment: C: IGV error: Error loading SAM header: For sequence 34711, text and binary have di
... All i did was mapping the reads onto transcriptome and obtained a sam file which is later converted into bam as I shown below. Is there any way to look which transcript_Id/Contig_Id got corrupted? or should I have to remap ...
written 22 months ago by EVR530
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Comment: C: IGV error: Error loading SAM header: For sequence 34711, text and binary have di
... My samtools version : 1.3 My IGV version: 2.3.97 Command for converting sam to bam file: > samtools view --threads 40 -F 4 -bS -o mySample.bam -O bam > mySample.sam Command for sorting: > samtools sort --threads 40 -o Sorted_mySamlpe.bam -O bam mySample.bam Command for indexing ...
written 22 months ago by EVR530
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IGV error: Error loading SAM header: For sequence 34711, text and binary have different lengths in file.
... HI, I have sam file and I converted into a bam and later sorted it. I also created bam index for the sorted_bam file. When I am trying to load the bam files into IGV, I am getting the following error: > Error loading SAM header: For sequence 34711, text and binary have > different lengths in ...
bam rna-seq igv written 22 months ago by EVR530 • updated 22 months ago by dyollluap300
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Finding fragemented transcriptome
... Hi, I have de novo assembled transcriptome genereated using trinity pipeline. I would like to know whether this de novo assembled transcriptome is fragmented or not. Thanks in advance ...
denovo_assembly transcriptome written 23 months ago by EVR530 • updated 23 months ago by Rohit1.3k
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Comment: C: Normalize bedtools gene coverage by total number of reads
... You can get the raw counts for your set of specific genes when you have Bam or SAM files. Later you can load the raw counts inot R and normalize using DESeq2 or EdgeR ...
written 24 months ago by EVR530

Latest awards to EVR

Popular Question 6 months ago, created a question with more than 1,000 views. For Counting reads within regions of interest
Popular Question 6 months ago, created a question with more than 1,000 views. For Identifying full length transcripts in a transcriptome
Popular Question 6 months ago, created a question with more than 1,000 views. For Generating GTF file for de novo assmebled transcriptome
Popular Question 6 months ago, created a question with more than 1,000 views. For Counting reads within regions of interest
Appreciated 11 months ago, created a post with more than 5 votes. For A: Finding UTR regions in the RNA sequencing data from a non-model organism
Popular Question 11 months ago, created a question with more than 1,000 views. For Counting reads within regions of interest
Popular Question 11 months ago, created a question with more than 1,000 views. For Identifying full length transcripts in a transcriptome
Popular Question 11 months ago, created a question with more than 1,000 views. For Generating GTF file for de novo assmebled transcriptome
Popular Question 11 months ago, created a question with more than 1,000 views. For Quality control for AB Solid fastq files
Popular Question 11 months ago, created a question with more than 1,000 views. For Splitting the y axis values in R plot
Popular Question 11 months ago, created a question with more than 1,000 views. For Counting mutated reads from RNA Seq data
Popular Question 11 months ago, created a question with more than 1,000 views. For Generating GTF file for de novo assmebled transcriptome
Great Question 13 months ago, created a question with more than 5,000 views. For High Sequence Duplication levels in FastQC
Student 13 months ago, asked a question with at least 3 up-votes. For High Sequence Duplication levels in FastQC
Popular Question 14 months ago, created a question with more than 1,000 views. For Generating GTF file for de novo assmebled transcriptome
Popular Question 14 months ago, created a question with more than 1,000 views. For Generating GTF file for de novo assmebled transcriptome
Popular Question 16 months ago, created a question with more than 1,000 views. For Generating GTF file for de novo assmebled transcriptome
Popular Question 17 months ago, created a question with more than 1,000 views. For Generating GTF file for de novo assmebled transcriptome
Scholar 17 months ago, created an answer that has been accepted. For A: How to find differentially expressed genes after mapping with Stampy?
Popular Question 18 months ago, created a question with more than 1,000 views. For Generating GTF file for de novo assmebled transcriptome
Popular Question 19 months ago, created a question with more than 1,000 views. For Counting mutated reads from RNA Seq data
Popular Question 20 months ago, created a question with more than 1,000 views. For Counting mutated reads from RNA Seq data
Popular Question 21 months ago, created a question with more than 1,000 views. For Counting mutated reads from RNA Seq data
Popular Question 21 months ago, created a question with more than 1,000 views. For Updating the Bowtie2 to version 2.2.5
Popular Question 2.2 years ago, created a question with more than 1,000 views. For High Sequence Duplication levels in FastQC

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