User: bipin

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bipin0
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Posts by bipin

<prev • 6 results • page 1 of 1 • next >
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What is the optimal read length filter for Kallisto post adapter removal?
... I am using 151bp **paired end** RNA seq reads to study differentially expressed genes between two conditions. The reads are aligned to a reference transcriptome using Kallisto(index created using default **kmer size of 31**). However ~16% of the reads have an adapter contamination with the adapte ...
kallisto rna-seq written 4 hours ago by bipin0
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Expected correlation between ATAC data and Chip-Seq histone marks
... I am analyzing a gene knockout dataset for which I have ATAC and Chip-seq data for the histone marks - H3K27Ac, H3K4me1 and H3K4me3. Since the histone marks represent enhancers is it correct to expect that the parts where we are getting a chip signal should also have an atac signal to indicate open ...
chip-seq atac-seq written 6 weeks ago by bipin0 • updated 6 weeks ago by i.sudbery2.3k
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Comment: C: Aligner for 50bp paired end short reads
... Thanks for your reply. Apologies I forgot to specify that I am using bowtie and not bowtie2 since I find it is recommended if the reads < 50 bp. The options I am giving to bowtie are `-k 2 -m 2 --best --strata`. The maximum insert size in my case is 600 so I was giving a slightly higher numbe ...
written 3 months ago by bipin0
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Aligner for 50bp paired end short reads
... I am aligning 50 bp paired-end data for ATAC seq. For aligning it to the reference genome I have tried bowtie with a larger insert size i.e. -X 1000 but the results are not optimal. Is there any other aligner which is expected to perform better for this input dataset? ...
assembly alignment chip-seq written 3 months ago by bipin0 • updated 3 months ago by colindaven700
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GSEA preranking metric for RNA Seq
... I came across multiple posts regarding the pre-ranking metric for GSEA when using RNA seq data. However, there doesn't seem to be a consensus. Some of the metrics I came across are:- - sign of log fold change * -log10(p-value[**not adjusted p-val**]) - logfc shrink values from DESeq2 - Inbuilt si ...
deseq2 rna-seq gsea written 4 months ago by bipin0 • updated 4 months ago by Kevin Blighe21k
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GSEA: Why is signal2noise suggested only for 3+ samples?
... The GSEA manual states that the signal2noise ranking metric should be used only in case of 3+ samples per condition. What is the reason for this restriction? I do understand that the denominator has standard deviations for the input values and it may be more meaningful in case of 3+ samples but ho ...
gsea rna-seq written 4 months ago by bipin0 • updated 4 months ago by h.mon15k

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