User: parashar.dhapola

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Posts by parashar.dhapola

<prev • 15 results • page 1 of 2 • next >
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Comment: C: HISAT2 end-to-end and --no-spliced-alignment mode returns gapped alignments
... Thanks for your reply Istvan. But RSEM is one of the revered tools for isoform quantification. If exclusion of gapped alignment is such a serious issue then, why has it not been highlighted in any literature for gene quantification. In fact newer tools like Kalliso used RSEM for most of benchmarki ...
written 2.8 years ago by parashar.dhapola150
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Answer: A: HISAT2 end-to-end and --no-spliced-alignment mode returns gapped alignments
... Solved it: Included following two parameters in HISAT2 run command to make gap opening and extension insanely difficult. --rdg 10000,10000 --rfg 10000,10000 My HISAT2 script now looks like this: INDEX=./indices/hisat/transcriptome FASTQ=$1 OUTPUT=./transcriptome_aligned/$2.sa ...
written 2.8 years ago by parashar.dhapola150
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HISAT2 end-to-end and --no-spliced-alignment mode returns gapped alignments
... I ran HISAT2 (index built using a transcriptome multi fasta) intending that it won't perform gapped alignment. I use following script to run HISAT: INDEX=./indices/hisat/transcriptome FASTQ=$1 OUTPUT=./transcriptome_aligned/$2.sam ./software/hisat-0.1.6-beta/hisat \ -q \ ...
hisat samtools rna-seq rsem written 2.8 years ago by parashar.dhapola150 • updated 2.8 years ago by Istvan Albert ♦♦ 78k
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Comment: C: Correlation of read count values from STAR and Kallisto
... Hello parashar.dhapola! We believe that this post does not fit the main topic of this site. Post closed For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why in a reply below, we' ...
written 2.8 years ago by parashar.dhapola150 • updated 12 weeks ago by RamRS19k
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Comment: C: Poor correlation of read count values from STAR and Kallisto
... Check out the latest update. It is quite interesting: Salmon actually has very high correlation with STAR+RSEM (r=0.98). You were definitely right about your tests. But this brings me back to original question: whats wrong with read count values from Kallisto? ...
written 2.8 years ago by parashar.dhapola150
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Comment: C: Poor correlation of read count values from STAR and Kallisto
... Dear Rob, I obtained annotation data from Ensembl release 83 [(FTP Link)][1]. I wrote a small piece of code (it was an overkill cause I tried to make a more Generic GTF parser, but it did its job right). You can review the code here: https://gist.github.com/parashardhapola/538589fd8b6a01eb2385 I ...
written 2.8 years ago by parashar.dhapola150 • updated 12 weeks ago by RamRS19k
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Comment: C: Poor correlation of read count values from STAR and Kallisto
... Thank for reply John, As you can see from updated post STAR counting strategy is not so bad after all. Bt this is nowhere near conclusive. I wish to see how Salmon performs here. ...
written 2.8 years ago by parashar.dhapola150
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Comment: C: Poor correlation of read count values from STAR and Kallisto
... Thanks for the reply Michael, I'm trying to use RSEM downstream of STAR. I don't want to take a naive read count approach (like HTSeq/Feature Count/easyRNA). I'm looking forward carrying out isoform based DE calling (EBSeq downstream of RSEM+STAR and Sleuth downstream of Kallisto). ...
written 2.8 years ago by parashar.dhapola150
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Comment: C: Poor correlation of read count values from STAR and Kallisto
... Dear Damian, Thanks for your reply. I' have got replicates and other samples in this datset. I'll share the results of those too. However, I'm not so sure about using any DE tool to make comparison. For example, DESeq is known to not play very well with Kallisto output. Hence, the compatibility of ...
written 2.8 years ago by parashar.dhapola150
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Correlation of read count values from STAR and Kallisto
... Hi, I'm analyzing a RNA-Seq dataset if yeast(GSE71712) using STAR and Kallisto. ...
correlation written 2.8 years ago by parashar.dhapola150

Latest awards to parashar.dhapola

Scholar 2.8 years ago, created an answer that has been accepted. For A: HISAT2 end-to-end and --no-spliced-alignment mode returns gapped alignments
Good Question 2.8 years ago, asked a question that was upvoted at least 5 times. For Correlation of read count values from STAR and Kallisto
Appreciated 2.8 years ago, created a post with more than 5 votes. For Poor correlation of read count values from STAR and Kallisto
Student 2.8 years ago, asked a question with at least 3 up-votes. For Poor correlation of read count values from STAR and Kallisto

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