User: eyonesi

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eyonesi50
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Posts by eyonesi

<prev • 25 results • page 1 of 3 • next >
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Conservation of lncrna
... Hello everybody Given that it is said that generally unlike protein-coding genes, which are usually conserved across the species, most lncRNAs are poorly conserved. Is it possible to identify lncrna based on conservation in other species with tools such as Blast? Or this methods are not ok.! Or if ...
rna-seq written 6 months ago by eyonesi50
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Comment: C: Snpcalling with replicates
... thank you for your answer they are biological replicates, do you mean that I create a bam file from my three biological replicates? Do I define them as a reads group? ...
written 7 months ago by eyonesi50
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Snpcalling with replicates
... Hello everybody I'm running snpcalling on RNASeq data. My data are related to 6 sample including two conditions, control and treatment with 3 replicates for each. I want to use the star aligner. I am confused at alignment step. Do I need to align three replicate of each condition with genome referen ...
snp written 7 months ago by eyonesi50 • updated 7 months ago by hafiz.talhamalik290
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Answer: A: GO and KEGG from DESeq2 counts
... GOseq is a suitable R package for GO AND KEGG enrichment. Maybe this link will help you related to DESeq2. https://wikis.utexas.edu/display/bioiteam/GO+Enrichment+using+goseq ...
written 7 months ago by eyonesi50
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Answer: A: RNA-Seq differential gene expression without biological and technical replicates
... Deseq, edgR and bayseq are pakages that can analyze without replicate. But, i think, they require replicate when running in the galaxy. Regardless of the galexy, edgR and Bayseq can be better choices for anlyses without replicat. ...
written 7 months ago by eyonesi50
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Comment: C: SNV and indel calling with RNA-seq data without a reference genome
... Dear sam Sorry for the delayed response. Star is a splice aware aligner and is suitable for the snp calling step. I am not sure. Perhaps other splice aware aligner, such as tophat, may also be appropriate. CLC is a comprehensive analysis package and very useful. I didn’t work with it and I don’t k ...
written 8 months ago by eyonesi50
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Answer: A: SNV and indel calling with RNA-seq data without a reference genome
... Hi, I am running a similar project. First to create reference transcriptome, you should assemble the reads by de novo assembler such asTrinity and Bridger. I guess you did this step because deferentially expressed genes are available to you. Then, the second step is to create supertranscripts and an ...
written 8 months ago by eyonesi50
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Comment: C: picard error in trinty pipeline
... hello, I was using Android and the icons were not shown, I hope I understood your guidance correctly. it's done now. thank you. ...
written 8 months ago by eyonesi50
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picard error in trinty pipeline
... Hi everybody, I am running GATK pipeline for variant calling in trinity with following command. /usr/local/bin/Trinityrnaseq-v2.6.6/Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py --st_fa ./SuperDuper.fasta --st_gtf ./SuperDuper.gff -p ./FCHG1.fq.gz ./FCHG.fq.gz -o ./varian ...
software error snp written 8 months ago by eyonesi50 • updated 8 months ago by JC12k
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Comment: C: interpretation of KEGG result
... hi all anyone have any ideas on this? thank you for help me ...
written 2.2 years ago by eyonesi50

Latest awards to eyonesi

Popular Question 6 months ago, created a question with more than 1,000 views. For minimum hardware requirement for denovo RNAseq analysis
Popular Question 6 months ago, created a question with more than 1,000 views. For to pool or not to pool
Scholar 6 months ago, created an answer that has been accepted. For A: GO and KEGG from DESeq2 counts
Popular Question 8 months ago, created a question with more than 1,000 views. For trinity installation command
Popular Question 2.2 years ago, created a question with more than 1,000 views. For trinity installation command

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