User: bioinfo_ga

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bioinfo_ga20
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Posts by bioinfo_ga

<prev • 27 results • page 1 of 3 • next >
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(Closed) DESeq2 normalised data
... I am trying to run DESeq2 script for Differential expression analysis. I am getting an output file with following columns "baseMean" "log2FoldChange" "lfcSE" "stat" "pvalue" "padj" I also need sample-wise normalised values as we obtain in DESeq. Is there any way to retrieve them? Thanks. ...
rna-seq written 24 days ago by bioinfo_ga20
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Flair error in nanopore data
... Hi all I am performing alternative splicing for nanopore data using tool FLAIR. In that there is a module, "find_alt3prime_5prime_ss.py" where i am getting continous error regarding usage. usage: script.py isoforms.psl colnum alt_acceptor.txt alt_donor.txt Can anyone elaborate the colnum paramete ...
rna-seq sequencing written 3 months ago by bioinfo_ga20
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Comment: C: Cuffdiff - Error in running cuffdiff by using the merged transcriptome assembly
... Try this if you have one control and one treated sample cufflinks-2.2.1.Linux_x86_64/cuffdiff -u -p 25 --library-type fr-firststrand -o /Cuffdiff/Control_VS_Treated /Cuffmerge/merged.gtf Control/A_Sorted.bam Treated/C_Sorted.bam, -L Control,Treated In case of replicates try the following command ( ...
written 4 months ago by bioinfo_ga20
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Comment: C: Cuffdiff 2.2.1 Segmentation fault: 11
... You can use DEseq2 for the same as it is more updated method ...
written 4 months ago by bioinfo_ga20
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Comment: C: sirna analysis database for plants
... can i download all plant sirna from RNACentral and do homology approach method (Blast) for pomegranate sequences maybe with e-5 ...
written 4 months ago by bioinfo_ga20
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sirna analysis database for plants
... Hi all I want to do sirna analysis for plant specie (pomegranate) can anyone suggest any database or source for downloading sirna sequences. Thanks ...
rna-seq written 4 months ago by bioinfo_ga20
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RAP IDs information required
... Hi i have performed transcriptome analysis in which reference used is oryza sativa indica species. I want RAP-Ids for the DE data. Is it possible to get RAP-IDs for indica species or are they available only for japonica species. Thanks ...
rna-seq written 4 months ago by bioinfo_ga20
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Answer: A: Help regarding RNAseq data analysis.
... You can refer to the following links: Genome: ftp://ftp.ensembl.org/pub/release-97/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz GTF: ftp://ftp.ensembl.org/pub/release-97/gtf/homo_sapiens/Homo_sapiens.GRCh38.97.chr.gtf.gz ...
written 5 months ago by bioinfo_ga20
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Motif identification in ripseq analysis
... Hi, I have performed ripseq analysis using ripseeker tool where i have identified the peaks (binding). I want to perform motif identification for the same. Kindly suggest any tool. Regards- ...
rna-seq written 5 months ago by bioinfo_ga20 • updated 5 months ago by ATpoint26k
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Comment: C: small rna length distribution
... I have used small rna workbench tool and used inbuilt adapter (LMN_3). I went through published papers of which almost all have reported the same trend (18-22bp). I checked for piwi RNA also but it is <0.02% in my data. ...
written 5 months ago by bioinfo_ga20

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Popular Question 4 months ago, created a question with more than 1,000 views. For Reason for multiple mapping of reads ?

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