User: taniamahmood38

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Posts by taniamahmood38

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Number of upregulated and downregulated genes from counts matrix
... Yes, trinity is a command line tool. It makes use of R packages for differential gene expression analysis (EdgeR, DSeq2, limma etc.) . Anyways, I am really grateful to you for the help. Many thanks. ...
written 7 days ago by taniamahmood3820
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Number of upregulated and downregulated genes from counts matrix
... Hi, I am doing differential gene expression analysis on two datasets using trinity toolkit. Now i have TMM expression counts matrix, MA plot, Volcano plot, heatmap etc. I want to know the exact number of upregulated and downregulated genes in my dataset. Is there any tool which can help to co ...
degs up and downregulated genes rna-seq written 8 days ago by taniamahmood3820
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Comment: C: Converting a BAM/VCF into genetic recombination map tsv file
... Sure, thank you so much. ...
written 29 days ago by taniamahmood3820
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Comment: C: Converting a BAM/VCF into genetic recombination map tsv file
... Many thanks for helping. This is the perfect file i want but i require GeneMap file of Goat (Capra hircus) instead of human. Is it possible to get that one for goat ? Sorry to trouble but this link contains the GeneMap file for human only. ...
written 4 weeks ago by taniamahmood3820
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Converting a BAM/VCF into genetic recombination map tsv file
... Hii, I am using Selscan for XPEHH, iHS analysis. For these tests, a genetic recombination map tsv file with four columns: (Chromosome, Position(bp), Rate(cM/Mb), Map(cM)) is required. Currently, i have a BAM file and a VCF file. If anyone please sort out how can i convert either my BAM or my VC ...
--genemap bam/vcf selscan .tsv file format written 4 weeks ago by taniamahmood3820
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Comment: C: Split synchronized file
... Thank you so much. I will surely try this. ...
written 12 months ago by taniamahmood3820
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Split synchronized file
... Hii, I have a synchronized file (output from popoolation2 tool using its feature mpileup2sync.jar). And i had merged 21 synchronized files of various breeds for downstream analysis. Now i want a single synchronized file from it. Please someone guide me how to extract/separate/split that merged sync ...
sync file ubuntu popoolation2 tool written 12 months ago by taniamahmood3820
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Comment: C: Convert BCF to BAM
... Sure i will try and thank you so much for your kind and quick responses @Pierre Lindenbaum. ...
written 13 months ago by taniamahmood3820
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Comment: C: Convert BCF to BAM
... when i run this command ./gradlew --stacktrace vcf2bam the error occurs is FAILURE: Build failed with an exception. * What went wrong: Could not create an instance of type org.gradle.initialization.DefaultSettings_Decorated. > Could not initialize class org.codehaus.groovy.runtime.InvokerHelpe ...
written 13 months ago by taniamahmood3820 • updated 13 months ago by Pierre Lindenbaum134k
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Comment: C: Convert BCF to BAM
... Ubuntu (Linux OS). Secondly i have put my jvarkit-master in java 11 folder and has given path to it. ...
written 13 months ago by taniamahmood3820

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