User: eyonesi
eyonesi • 30
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Posts by eyonesi
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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
eyonesi • 30
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... 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 ...
written 8 days ago by
eyonesi • 30
• updated
7 days ago by
hafiz.talhamalik • 240
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... 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
eyonesi • 30
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... 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
eyonesi • 30
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... 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
eyonesi • 30
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... 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
eyonesi • 30
0
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2
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145
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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
eyonesi • 30
10
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... 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 ...
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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
eyonesi • 30
0
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... 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 ...
written 20 months ago by
eyonesi • 30
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Popular Question
7 weeks ago,
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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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