User: mathavanbioinfo

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Posts by mathavanbioinfo

<prev • 48 results • page 1 of 5 • next >
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DEGS analysis with DESeq2?
... Hello all, I am working in DEG analysis using DESeq2, I followed the protocol given in StringTie, the results file has very **few genes** ( mapped with AnnotationDbi,org.Hs.eg.db), and the genes start with **MSTRG** abundantly present. Is there any way to map MSTRG id gene ids or how to deal with ...
deseq2 degs written 2 days ago by mathavanbioinfo50
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DEGs analysis with StringTie results?
... Hello All, I am working on differential gene expression analysis using the stringTie assembly tools. For count matrix, prepDE generating two files **gene_count_matrix** and **transcript_count_matrix**. As per the protocol they have used the gene_count_matix file for the DEGs analysis. Is it possible ...
stringtie degs deseq2 written 2 days ago by mathavanbioinfo50
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Comment: A: construction of draft genome from the contigs
... The genome size approximately 19kb in size ...
written 20 days ago by mathavanbioinfo50
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Comment: A: How to get GTF file for Rousettus_aegyptiacus?
... https://ibb.co/1KQbrB7 ...
written 22 days ago by mathavanbioinfo50
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Comment: C: How to get GTF file for Rousettus_aegyptiacus?
... Thank you very much for the response Response from stringTie **Please make sure the -G annotation file uses the same naming convention for the ge ...
written 22 days ago by mathavanbioinfo50
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How to construct draft genome of virus using Trinity de novo assembler?
... Hi, I am working on the viral genome ( Single negative-stranded RNA virus) and the reads generated are from the ion torrent ( Amplicons) method. After performing de novo assembly using trinity tool produced contigs are in the form of a single fasta file. The next step is to construct a draft genome ...
rna virus trintiy amplicons written 22 days ago by mathavanbioinfo50
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Comment: C: How to get GTF file for Rousettus_aegyptiacus?
... Thanks for the response Can you recommend to use gffread package for the convertion of gff to gtf ...
written 23 days ago by mathavanbioinfo50
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How to get GTF file for Rousettus_aegyptiacus?
... Hello Biostars, I am working on the genome analysis of Rousettus_aegyptiacus organisms from data obtained ENA database. After the quality checking (Fastqc) of the reads, I have done alignment with hiasat2, index building carried out using the file from NCBI: ftp://ftp.ncbi.nih.gov/genomes/Rousettus_ ...
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How to extract 3', 5' UTR sequences from genbank records using python, PERL and R code?
... Hello All, I have 1000 sequences of genebank records, I want to extract the only 3'UTR, 5'UTR sequences from the sequences and to store in excel format. Share your ideas and suggestion [using PERL or Python or R codes] ...
utr written 7 weeks ago by mathavanbioinfo50 • updated 6 weeks ago by zubenel30
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Comment: C: Is virus specific UTR prediction tool available?
... Thank you for this information ...
written 8 weeks ago by mathavanbioinfo50

Latest awards to mathavanbioinfo

Scholar 22 days ago, created an answer that has been accepted. For A: How to get GTF file for Rousettus_aegyptiacus?
Popular Question 5 months ago, created a question with more than 1,000 views. For Up and Down regulated genes
Popular Question 8 months ago, created a question with more than 1,000 views. For Up and Down regulated genes
Popular Question 9 months ago, created a question with more than 1,000 views. For Up and Down regulated genes
Popular Question 9 months ago, created a question with more than 1,000 views. For Up and Down regulated genes
Popular Question 18 months ago, created a question with more than 1,000 views. For Up and Down regulated genes
Popular Question 24 months ago, created a question with more than 1,000 views. For Up and Down regulated genes
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Microarray adata Normalization using GEO2R?

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