User: amitunited0532

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Posts by amitunited0532

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Comment: C: How to get the alignment summary of HISAT2
... Can I find alignment summary after completing job, I mean from SAM file ? ...
written 4 months ago by amitunited053210
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Problem in analysis of Ballgown output by R (why q value are same in result ? )
... Hello, I have performed an RNAseq experiment, for which I used HISAT2 for the alingment, Stringtie for the assembly and the R package Ballgown for the Differential Expression (DE) analysis. After generation of differential expression table, I found q value is mostly same for all genes which is give ...
R ballgown differential expression (de) analysis written 5 months ago by amitunited053210 • updated 5 months ago by ATpoint14k
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(Closed) Gene enrichment analysis
... Please suggest better tools for Gene ontology or enrichment analysis for DEG. ...
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Comment: C: (ERR): bowtie2-align exited with value 1
... Use Hisat2, it is better and fast. or If you have better computational facility, go for STAR aligner. (Required at least 32GB RAM) I don't recommend Bowtie2 or tophat for your work. All the best ...
written 6 months ago by amitunited053210
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Comment: C: R package installtion error
... How can get administrator permission in R studio? ...
written 7 months ago by amitunited053210
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(Closed) R package installtion error
... When i gonna install packages it showing error like this. trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/survival_2.42-3.zip' Content type 'application/zip' length 4396605 bytes (4.2 MB) downloaded 4.2 MB trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/ ...
r studio R bioconductor r packages written 7 months ago by amitunited053210 • updated 7 months ago by finswimmer11k
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Comment: C: Mapsplice 2 error
... I kept all files in one folder and also checked command which suggested. Again showed same error. ...
written 7 months ago by amitunited053210
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Mapsplice 2 error
... When running this command it shows error like this, I have all file in One folder. Please help me to resolve this problem mapsplice.py -o outfuse --fusion --min-fusion-distance 200 -c bowtie2index.fa -x bowtie2index -1 SRR087416.fastq_filtered ---------------------------------------- ...
ngs data analysis rna seq fusion gene written 7 months ago by amitunited053210 • updated 7 months ago by EagleEye6.2k
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Comment: C: Mapsplice commands for fusion gene and which file used ?
... Output of mapsplice. [Sat Aug 4 12:29:43 2018] Beginning Mapsplice run (MapSplice v2.2.0) [Sat Aug 4 12:29:43 2018] Bin directory: /home/prashant/anaconda2/bin/ [Sat Aug 4 12:29:43 2018] Preparing output location outputfusegene/ [Sat Aug 4 12:29:43 2018] Checking files or directory: SRR085725. ...
written 7 months ago by amitunited053210
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Mapsplice commands for fusion gene and which file used ?
... I have confused Which file used as reference genome (.fasta, fa, gtf, etc.) Please tell me about exact command with example, if possible. ...
mapsplice fusion gene rna-seq written 7 months ago by amitunited053210 • updated 7 months ago by archana.bioinfo87100

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