User: spriyansh29

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spriyansh2930
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Posts by spriyansh29

<prev • 14 results • page 1 of 2 • next >
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Does the expression data from GEO Series Matrix File(s) can directly be used with limma workflow
... I have to perform differential gene expression analysis using ````limma````. Can I use GEO Series Matrix File(s) (expression set) in the limma workflow (differential expression analysis) without actually extracting the expression set from raw ````.CEL```` files. As I can see that ````limma```` work ...
normalization rma micro-array limma R written 13 days ago by spriyansh2930 • updated 13 days ago by Kevin Blighe59k
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Comment: C: Differential Gene Expression Analysis with low biological replicates
... I am quite new to RNA-Seq so I followed tutorials from bioconductor's website.For DESeq2 I have used ````DESeq(dds)```` and ````DESeq(dds, test="LRT", reduced = ~ 1)````. For EdgeR I have used ````glmQLFTest(fit,coef="Group2")```` and ````glmLRT(fit,coef=""Group2"")````. The plots are [Heatmap with ...
written 17 days ago by spriyansh2930
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Answer: A: STAR error (segmentation fault) in Aligning reads
... It was a hardware constraint, as STAR requires a minimum of 30Gigs of RAM. ...
written 17 days ago by spriyansh2930
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Differential Gene Expression Analysis with low biological replicates
... I have two groups with 12 (6 + 6) samples that were generated from bulk-RNA-Seq experiments. While performing the differential expression analysis the adjusted-p-value came out to be 1 with both DESEQ2 (Wald, LRT) and EdgeR (Quasi-likelihood, LRT). After, skimming through a few posts and papers, I f ...
R ngs differential-expression rna-seq written 17 days ago by spriyansh2930
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Comment: C: Alignment with multiple reference genome using HISAT2
... I am actually new to NGS analysis, and that "cat technique worked well for me. I wanna know that while extracting the read counts from the .bam files how should I proceed with the ht-seq count? 1) Should I extract read counts using 3 different GFF/GTF files (3 for 3 genomes as used in alignment) and ...
written 20 days ago by spriyansh2930
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Comment: C: Alignment with multiple reference genome using HISAT2
... well, I think it will work, as all the 3 genomes are viral so they would take less space. I will give it a try and update! ...
written 20 days ago by spriyansh2930
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Alignment with multiple reference genome using HISAT2
... I have 3 reference genomes and I wish to align my FASTQ reads against all 3 of them. I have used ````hisat2-build```` to build individual indexes of all 3 of them, but couldn't find the command to make an index of multiple genomes. I have run the following command for alignment - ````hisat2 -p 4 ...
assembly next-gen rna-seq alignment hisat2 written 20 days ago by spriyansh2930
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Location of Genes on Chromosome
... I have a list of Genes (Ensemble ids). I need to find their locations in the human chromosomes. Information that I need- Start location Stop Location Length I have tried ShinyGo but got only a graph with the location of genes on the chromosome but not exact locations. ...
gene chromosomal-mapping mapping chromosome written 3 months ago by spriyansh2930 • updated 4 weeks ago by Biostar ♦♦ 20
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Comment: C: STAR error (segmentation fault) in Aligning reads
... I have used with R1 and R2 reads together as they are forward/reverse reads. Also, where I could find the log for STAR, I have installed it using 'make STAR' ...
written 5 months ago by spriyansh2930
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Comment: C: STAR error (segmentation fault) in Aligning reads
... Yes, I did, I used it along with GATK and samtools as follows, samtools faidx ebola_ref.fasta gatk CreateSequenceDictionary --REFERENCE ebola_ref.fasta --OUTPUT=ebola_ref.dict STAR --runMode genomeGenerate --genomeDir ../genomedir/ --genomeFastaFiles --genomeSAindexNbases 6 ebola_ref.fasta --run ...
written 5 months ago by spriyansh2930

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Student 6 months ago, asked a question with at least 3 up-votes. For Identification of Human Genes ?

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