User: kousi31

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kousi310
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Posts by kousi31

<prev • 44 results • page 1 of 5 • next >
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Comment: C: How to get multiple alignments from different species using lastz?
... Pre-computed alignments are not available for domestic water buffalo (Bubalus bubalis) in UCSC or ensemble. I want to create a maf file for buffalo with human, cow and dog. Is there any tutorial links on how to perform multiple alignment on genomes? What may be memory requirement to do the same? ...
written 4 weeks ago by kousi310
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Which axis to look for in PCA plot to understand the sample clustering
... Hi all, I have four replicates for early and late lactation stages each. I did rlog transformation of the htseq counts and did PCA as a QC step to know whether the biological conditions cluster together. I obtained the attached PCA plot. Now I have a confusion on the axis I have to look for. As in ...
pca qc rna-seq clustering written 4 weeks ago by kousi310 • updated 4 weeks ago by swbarnes26.5k
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Comment: C: Doubt - installing LncTar software
... Thank you for your suggestions. ...
written 4 weeks ago by kousi310
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Comment: C: Doubt - installing LncTar software
... I tried `cpan App::cpanminus` then `sudo cpanm Genecare::PerlOligos` Got error > Finding Genecare::PerlOligos on cpanmetadb failed. ! Finding > Genecare::PerlOligos () on mirror http://www.cpan.org failed. ! > Couldn't find module or a distribution Genecare::PerlOligos The link sa ...
written 4 weeks ago by kousi310
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Doubt - installing LncTar software
... Hi all, I want to install LncTar software. I have downloaded LncTar as compressed file. I extracted the folder. The folder has LncTar.pl file and Genecare folder Inside the Genecare folder there is a file named - PerlOligos.pm when I run the command `perl LncTar.pl -p 1 - l Examp1_RNA1. ...
perl software installation lnctar written 4 weeks ago by kousi310 • updated 4 weeks ago by h.mon27k
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Comment: C: How to obtain multiple sequence alignments of genomes of selected vertebrate spe
... Can you please tell me what would be the RAM requirement, If I attempt to do a pairwise alignment between human and buffalo genome (2.7 GB) using LASTZ?.. ...
written 5 weeks ago by kousi310
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FIRE installation error
... Hi all, I am trying to install FIRE. I have installed pcre-8.42 in the directory `/usr/local/src.` But upon running `./configure` I get the error > "Attention: you don't appear to have libpcre installed on your > machine." I ran `sudo sh install-pcre.sh`(provided by the software itself) ...
software error written 6 weeks ago by kousi310
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Comment: C: How to obtain multiple sequence alignments of genomes of selected vertebrate spe
... A clear tutorial. I need water buffalo (Bubalus bubalis) and it is not in ensemble too. ...
written 6 weeks ago by kousi310
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How to obtain multiple sequence alignments of genomes of selected vertebrate species?
... Hi all, I want multiple sequence alignments of few vertebrate species (Human, cow, buffalo, sheep and goats). UCSC browser has MSA for 46 vertebrate species and MSA of 3 or 4 species under individual species. But I don't find the combination I need. Is it possible to extrat MSA of desired species ...
multiple sequence alignment written 6 weeks ago by kousi310 • updated 6 weeks ago by andrew.j.skelton735.8k
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Comment: C: How to quantify gene expression when stringtie considers two adjacent genes as s
... Thank you for your patient suggestions. ...
written 7 weeks ago by kousi310

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