User: rohitsatyam102

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Posts by rohitsatyam102

<prev • 114 results • page 1 of 12 • next >
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Comment: C: DRIMSeq with more than 2 categories in the group
... Hi @poecile.pal Were you able to figure this out? I also have a similar situation. I have data from 5 different layers of a plant (each having 3 replicates) collected at different days of flowering 4, 8, 10, 16. ...
written 9 days ago by rohitsatyam102200
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RNAseq of rice is super weird
... Hi Peeps!! Something has been really troubling me about a public dataset that I am currently working on. The sequencing quality was of course not very great and there were many reads containing runs of As and Ts. What was super weird was when I switched from an older rice genome reference of 2011 p ...
genome sequence rna-seq written 11 days ago by rohitsatyam102200
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What packages/tools are available to use SJ.out.tab file obtained from STAR
... Hi everyone. I have these `Sj.out.tab` files obtained from STAR and am aware that these files contain high confidence collapsed splice junctions. However, I failed to find tools/R packages that take these files as input and help you do some meaningful analysis like differential splicing. Can you po ...
R next-gen sequence rna-seq written 14 days ago by rohitsatyam102200 • updated 12 days ago by brown.annaleigh10
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Comment: C: AGAT - Another Gff Analysis Toolkit
... Wonderful. Indeed they had identical exon start and end and transcript st too. Thanks Jacques. You really saved the day. The AGAT was otherwise smooth and took care of the problems we were previously facing with other converters. Thanks a load again. ...
written 15 days ago by rohitsatyam102200
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Comment: C: AGAT - Another Gff Analysis Toolkit
... Hi Juke34 I am using AGAT for a gff3 to gtf conversion and I saw some of the isoforms removed "28 identical isoforms removed". Why should an isoform be removed, I don't understand especially if gtf has to be used in RNASeq. Will it make any difference in the counts' quantification both for genes an ...
written 16 days ago by rohitsatyam102200
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Comment: C: GO annotation for rice in an R package
... Hi @djyjin Were you able to figure this out? I am experiencing a similar challenge ...
written 17 days ago by rohitsatyam102200
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Comment: C: EnhancedVolcano questions on parameters, arguments can set
... Hi Kevin. I really appreciate the functionality that your package provides but I am experiencing an issue while making Volcano plots. When I use the results obtained after lfcshrinkage, and feed them to EnhancedVolcano for the plot, I observe that for some reason, statistically significant genes do ...
written 18 days ago by rohitsatyam102200
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Comment: C: DESeq2 compare all levels
... Hi Kevin Thanks for the solution you offered for pairwise comparison. During lfcshrinkage, when I try using apeglm method it throws the following error >AL_exp1_vs_SE_exp1 <- lfcShrink(dds, contrast=c("Comparison", "AL_exp1", "SE_exp1"), res=AL_exp1_vs_SE_exp1, type="apeglm") Error in l ...
written 18 days ago by rohitsatyam102200
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Comment: C: Sjdboverhang Option In Star
... We have two dataset. One dataset is generated in our lab and has 58 read length and other dataset obtained from a paper which contains read length of 75bp. In such case what should be the value of sjdboverhang ...
written 21 days ago by rohitsatyam102200
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Comment: C: Does it matters whether we give FASTA or FASTq files to STAR
... So it does take Basequality into consideration. So saying this wouldn't be wrong that FASTQ files must be preferred over FASTA files? ...
written 22 days ago by rohitsatyam102200

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