User: aiswaryabioinfo

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Posts by aiswaryabioinfo

<prev • 21 results • page 1 of 3 • next >
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multi-factor Deseq LRT test analysis
... Hi All, I need help to resolve the design to get differentially expressed gene with deseq2. I have two cultivars (R and S), three time points (1day, 3day and 7day) and two treatments (Control, Treated) with two replicates each. I have a total of 24 samples. I need to compare: R Vs S due Treate ...
deseq2 design rna-seq lrt written 4 weeks ago by aiswaryabioinfo20 • updated 4 weeks ago by tiago2112871.2k
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Compare pairs of key/value of perl hash tables in thre input files
... Does anyone know how to compare pairs of key/value in two hashtables with a third file ? I'm currently working with three tab delimited files. The first two files contains the list of proteins with their pfam domain ids as information and the third file contains the domain-domain interactions. I nee ...
hash table perl protein domain unix hashes written 3 months ago by aiswaryabioinfo20 • updated 3 months ago by JC11k
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how to calculate pfamscan.pl results alignement coverage?
... How can I calculate aligned sequence length coverage from the results of protein domains obtained through pfam_scan.pl program. The result consist of columns such as input seqs_id alignment start and end envelope start and end hmm_accession hmm_name type hmm start and end (I don't know) ...
domain alignment protein coverage pfamscan written 3 months ago by aiswaryabioinfo20
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Comment: C: Alternative tool for split'N'trim
... Sir, I dont have much computational facility to run RNA-seq variant calling in computer so I am relaying onlie platforms like galaxy. In order to preprocess the aligned BAM file I marked the duplicates with Picard. now for splitting I am not getting any online tools. So Can anyone of you help me out ...
written 4 months ago by aiswaryabioinfo20
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Alternative tool for split'N'trim
... I am trying to identify SNPs from RNA-Seq data. Is there any alternative tool for split'N'trim in usegalaxy server ...
rna_seq galaxy single cell snp written 4 months ago by aiswaryabioinfo20
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Comment: C: How to draw a chromosome graph with only selected genes marked in it
... Thank you sir, this will really help me. I only want to make the map of one single chromosome with highlighting certain specific genes in that chromosome. I will try your suggestions. ...
written 14 months ago by aiswaryabioinfo20
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Comment: C: How to draw a chromosome graph with only selected genes marked in it
... I have checked karyoploteR but it is not serving my purpose my data is like this gene chromosome start end gene1 4 20 3000 gene2 4 4000 5000 gene3 4 6000 7000 I want to mark this genes in corresponding chromosome and make a gra ...
written 14 months ago by aiswaryabioinfo20 • updated 14 months ago by RamRS30k
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How to draw a chromosome graph with only selected genes marked in it
... Dear all, I need to draw a linear chromosome graph for a specific chromosome with marking selected genes segments instead of the whole chromosome. My chromosome is having a size of 135.06mb (genbank file size: 181mb) I could find online tools like "ogdraw" which are specific for organelles like ch ...
genome chromosome visualization map tool written 14 months ago by aiswaryabioinfo20 • updated 14 months ago by bernatgel2.6k
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Comment: C: DESeq2 compare all levels using wald and lrt test
... Hi Devon, I got the error as typo Is it necessary to use lfcshrink() in all_vs_all design comparison. Will it affect in identification of significant genes? What affect lfcshrink () will have in the expression values of genes? I tried the all_vs_all design comparison in DESeq2 (Version 2.11.40.2) ...
written 15 months ago by aiswaryabioinfo20
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DESeq : base mean value are same for all genes in all the three combinations in compare all levels design
... My RNA-seq dataset consist of Resis_treated (1st day, 3rd day and 7th day) samples taken under 3 time point with 2 replicated for each time point. I have a condition with 3 levels (day1, day3, day7). I used HTseq-count to get the read counts. I am trying to get the DEGs between Day3VsDay1, Day7VsDa ...
R deseq2 log2fc base mean written 15 months ago by aiswaryabioinfo20 • updated 15 months ago by h.mon31k

Latest awards to aiswaryabioinfo

Popular Question 10 weeks ago, created a question with more than 1,000 views. For How to get Gene Co-expression Network from RNA seq data using cor() function?
Popular Question 3 months ago, created a question with more than 1,000 views. For DESeq2 compare all levels using wald and lrt test
Popular Question 13 months ago, created a question with more than 1,000 views. For How to get Gene Co-expression Network from RNA seq data using cor() function?

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