User: Ankita.narang86

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Posts by Ankita.narang86

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Comment: C: Gene(s) withTpm value(s) zero in kallisto though reads are mapped
... Hi, Thanks a lot for sharing link on - Why you should use alignment-independent quantification for RNA-Seq. I compared transcript vs gene abundances (since I m working on novel organism, I am not very sure of accuracy of transcriptome model as well ), I used gene and transcript coordinates and com ...
written 5 weeks ago by Ankita.narang860
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Comment: A: Gene(s) withTpm value(s) zero in kallisto though reads are mapped
... Hi, Thanks a lot for sharing link on - Why you should use alignment-independent quantification for RNA-Seq. I compared transcript vs gene abundances (since I m working on novel organism, I am not very sure of accuracy of transcriptome model as well ), I used gene and transcript coordinates and com ...
written 5 weeks ago by Ankita.narang860 • updated 5 weeks ago by genomax55k
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Comment: C: Gene(s) withTpm value(s) zero in kallisto though reads are mapped
... I didn't check for this region but i m sure the region has more than 100 reads, all are multi-mapped is less probable. ...
written 6 weeks ago by Ankita.narang860
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Gene(s) withTpm value(s) zero in kallisto though reads are mapped
... Hi, I have paired end stranded rnaseq data (trueseq stranded dutp protocol), Intially i incorrectly used - - fr option instead of rf. However, even with correct rf option for this protocol, i noticed that expression of a gene i was looking at is zero (rna direction is 3' to 5'), though are enough ...
gene alignment rna-seq written 6 weeks ago by Ankita.narang860
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Comment: A: RNASeq DGE : Kallisto-sleuth Vs Ballgown
... Thanks everyone !! your answers are insightful and help me to pursue in a meaningful direction. ...
written 9 weeks ago by Ankita.narang860
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RNASeq DGE : Kallisto-sleuth Vs Ballgown
... Hi all, I want to understand - How sleuth is different from ballgown when we do differential gene expression analysis [apart from alignment free vs alignment based reasons]. When i compared both of them, i got reasonably good number of DGEs with sleuth, however, with ballgown i didn't get any di ...
next-gen rna-seq written 10 weeks ago by Ankita.narang860
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Regarding analysis of stranded RNASeq [TrueSeq , dUTP protocol]
... I have to identify lncRNAs [A pilot study with 4 samples in total I am using Hisat2 and Stringtie for aligning and to find transcripts respectively. I have used intially library type mode --fr (unknowingly) and did analysis and after reading some papers and blogs I realised I have to use --rf rathe ...
alignment rna-seq written 12 weeks ago by Ankita.narang860

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