User: Apex92

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Apex9220
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6 hours ago
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1 year, 3 months ago
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m*****************@scilifelab.se

Posts by Apex92

<prev • 23 results • page 1 of 3 • next >
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Why do I see 3-nucleotide periodicity in RNA-Seq?
... Hi everyone. I have a question regarding one of my plots that I made out of a bam file. We have performed the ```RNA-Seq``` and after the```bowtie alignment```, I tried to plot the frequency of each leftmost (4th column in bam file) nucleotide position for the mapped reads. In this way, I tried to f ...
alignment next-gen rna-seq sequencing written 18 days ago by Apex9220
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Comment: C: How to bin a genome to different regions
... Basically, my purpose is to make my own gtf file to be able to find the differentially expressed regions in the genome. So that is the reason I want to do the binning and then make a gtf file out of it. ...
written 19 days ago by Apex9220
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Comment: C: How to bin a genome to different regions
... Dear @Alex thank you for your detailed answer. I was wondering whether it will be possible to convert the binned genome to a gtf file. I have my purpose of binning the genome here in this link ```https://www.biostars.org/p/465603/#465608``` ...
written 20 days ago by Apex9220
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Comment: C: Get chromosome sizes from fasta file
... ALSo can be in this format at once: ```samtools faidx genome.fa | cut -f1,2 > chromsizes``` ...
written 21 days ago by Apex9220
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How to make a customized gtf file for differential expression purposes
... Hi everyone. I need to perform one analysis but not clear how should I start and go through it step by step. It would be great if you share some hints with me. My purpose is to do differential gene expression analysis but by making my own annotation file. So basically I have my mouse genome ```G ...
R next-gen sequence rna-seq alignment written 21 days ago by Apex9220
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Comment: C: How to bin a genome to different regions
... Could you please provide a link? It seems that there is no detailed manual about the ```bedtools makewindows```. ...
written 21 days ago by Apex9220
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How to bin a genome to different regions
... Hi, this is my first time binning a genome, it would be great to get some help from you experts. I have the mouse genome ```GRCm38.p6.genome.fa``` and I would like to bin this to ~2.5 million regions that are each 1000 nts long. With a bit of online searching, I figured out probably I have to us ...
genome binning rna-seq sequencing written 21 days ago by Apex9220 • updated 21 days ago by Alex Reynolds31k
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Comment: C: Error loading BAM on IGV
... Thank you @Pierre Yes as you mentioned the error was due to the ```commas```. I deleted them and did indexing and alignment again, it worked fine. ...
written 25 days ago by Apex9220
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Error loading BAM on IGV
... I get an error while uploading BAM file. I used bowtie to map small-RNA reads against one mRNA fasta file. I sorted and indexed the bam file but I get the error in uploading it on IGV: ```Error loading BAM file: htsjdk.samtools.SAMException: Sequence name 'X64322.2:1-409,510-527,628-676,777-1929' d ...
software error bam igv written 25 days ago by Apex9220 • updated 25 days ago by Pierre Lindenbaum131k
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Comment: C: -m option of HTSeq in featureCounts
... Thank you for the comment. With that being said, I go with the default version of alignment mode in featureCounts, is it ok? ...
written 3 months ago by Apex9220

Latest awards to Apex92

Scholar 5 months ago, created an answer that has been accepted. For A: Error with using getBM function in biomaRt
Scholar 5 months ago, created an answer that has been accepted. For A: Error with using getBM function in biomaRt

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