User: eyonesi

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eyonesi30
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Posts by eyonesi

<prev • 24 results • page 1 of 3 • next >
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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 days ago by eyonesi30
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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 8 days ago by eyonesi30 • updated 7 days ago by hafiz.talhamalik240
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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 26 days ago by eyonesi30
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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 28 days ago by eyonesi30
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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 6 weeks ago by eyonesi30
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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 6 weeks ago by eyonesi30
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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 7 weeks ago by eyonesi30
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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 7 weeks ago by eyonesi30 • updated 7 weeks ago by JC11k
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Comment: C: interpretation of KEGG result
... hi all anyone have any ideas on this? thank you for help me ...
written 20 months ago by eyonesi30
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interpretation of KEGG result
... Hi all I'm doing denovo RNAseq on a non-model plant under abiotic stress. I've done kegg enrichment for DE transcript by KAAS. But my results showed that in some cases there are several transcripts for a K-identifier or enzyme that can be the isoforms of a different gene or single gene based on th ...
rna-seq written 20 months ago by eyonesi30

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Popular Question 7 weeks ago, created a question with more than 1,000 views. For trinity installation command
Popular Question 20 months ago, created a question with more than 1,000 views. For trinity installation command

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