User: harikrishnanc903

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Posts by harikrishnanc903

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ABsolute Immune Signal (ABIS) deconvolution output
... I am currently working on the ABIS deconvolution method to find the immune cell type. I am not sure about the values obtained from the deconvolution of the TPM matrix. For example, quantiseq method provides cell fraction after deconvolution, like that what is the value in ABIS deconvolution. It woul ...
deconvolution rna-seq written 7 months ago by harikrishnanc9030
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Comment: C: How to get strand information in the bed file of macs1.4 peak calling output?
... Thanks. I have one more doubt. Homer does peak calling using the "findpeak".In homer output, we are getting strand information. Is it because homer uses a different algorithm to call the peak? ...
written 23 months ago by harikrishnanc9030
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Comment: C: How to get strand information in the bed file of macs1.4 peak calling output?
... From macs output(bed file), I have contig start and end position. I will use this information to extract the sequence from the genome. I am concerned about whether we need the stand information in the bed file for doing the same. ...
written 23 months ago by harikrishnanc9030
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How to get strand information in the bed file of macs1.4 peak calling output?
... I am new to MACS peak calling. **I am not sure how to get the strand information in the bed output file after running macs tool.** Using the strand information I need to extract the sequence from the genome. Any suggestion to add the strand information in the MACS output? ...
next-gen chip-seq written 23 months ago by harikrishnanc9030 • updated 22 months ago by ZZzzzzhong210
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How to set 1Kb resolution for Hi-C Juicebox Visualization
... I am using Homer tool to identify contact matrix in the genome. For visualization of contact matrics, I am using Juicebox. Using pre I have created Hi-C file from maketagdirectory. **In Jucier tool the pre-command bin the reads at 9 base-pair-delimited resolutions: 2.5M, 1M, 500K, 250K, 100K, 50K, 2 ...
next-gen chip-seq written 23 months ago by harikrishnanc9030
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GlimmerHMM giving Segmentation fault during gene prediction
... I am trying to do gene prediction using GlimmerHMM. Training model was successfully completed but during prediction its giving "segmentation fault". command : glimmerhmm_linux_x86_64 input.fasta -d Directory -o glimmer_results.gff -g Kindly give suggestions. ...
gene glimmerhmm prediction written 2.8 years ago by harikrishnanc9030

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Popular Question 20 months ago, created a question with more than 1,000 views. For GlimmerHMM giving Segmentation fault during gene prediction

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