User: taniamahmood38
taniamahmood38 • 20
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Posts by taniamahmood38
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... 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
taniamahmood38 • 20
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... 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 ...
written 8 days ago by
taniamahmood38 • 20
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... Sure, thank you so much. ...
written 29 days ago by
taniamahmood38 • 20
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... 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
taniamahmood38 • 20
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... 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 ...
written 4 weeks ago by
taniamahmood38 • 20
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C: Split synchronized file
... Thank you so much. I will surely try this. ...
written 12 months ago by
taniamahmood38 • 20
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... 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 ...
written 12 months ago by
taniamahmood38 • 20
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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
taniamahmood38 • 20
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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
taniamahmood38 • 20
• updated
13 months ago by
Pierre Lindenbaum ♦ 134k
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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
taniamahmood38 • 20
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