User: bioinfo_ga

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bioinfo_ga20
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Posts by bioinfo_ga

<prev • 32 results • page 1 of 4 • next >
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Comment: C: Difference in Human reference build p.10 and p.13
... ohh i see, ok let me see both the files. Thanks for the help. ...
written 4 months ago by bioinfo_ga20
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Comment: C: Difference in Human reference build p.10 and p.13
... From Ensembl database : [http://www.ensembl.org/Homo_sapiens/Info/Index] ...
written 4 months ago by bioinfo_ga20
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Difference in Human reference build p.10 and p.13
... Hi, For Human analysis as there has been update in the reference genome (GRCh38)build version from p10 to p13, i observed a drastic change in terms of the genome size as p.10 was 3 GB whereas p13 is 60 GB, what is the reason? Thanks. ...
rna-seq written 4 months ago by bioinfo_ga20
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Comment: C: Tophat2 command analysing
... tophat-2.0.13.Linux_x86_64/tophat -G ref.gtf --output-dir out index_prefix input_reads.[fasta|fastq]] Try using this command ...
written 10 months ago by bioinfo_ga20
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Any information on MAR-RNA
... Hi all I am looking for any details about MAR-RNA (matrix attachment region) analysis. What pipeline can be followed and what type of analysis can be done. ' Thanks ...
next-gen rna-seq written 10 months ago by bioinfo_ga20
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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 12 months 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 15 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 15 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 15 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 16 months ago by bioinfo_ga20

Latest awards to bioinfo_ga

Popular Question 9 months ago, created a question with more than 1,000 views. For Unexplained reads from a genome
Popular Question 9 months ago, created a question with more than 1,000 views. For Zero expression in cuffdiff
Popular Question 15 months ago, created a question with more than 1,000 views. For Reason for multiple mapping of reads ?

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