User: spriyansh29
spriyansh29 • 30
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- 1 year, 2 months ago
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Posts by spriyansh29
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2
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... 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 ...
written 13 days ago by
spriyansh29 • 30
• updated
13 days ago by
Kevin Blighe ♦ 59k
0
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... 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
spriyansh29 • 30
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216
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... It was a hardware constraint, as STAR requires a minimum of 30Gigs of RAM. ...
written 17 days ago by
spriyansh29 • 30
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... 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 ...
written 17 days ago by
spriyansh29 • 30
0
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1
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103
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... 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
spriyansh29 • 30
0
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... 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
spriyansh29 • 30
2
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1
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103
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1
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... 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 ...
written 20 days ago by
spriyansh29 • 30
0
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2
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161
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... 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. ...
written 3 months ago by
spriyansh29 • 30
• updated
4 weeks ago by
Biostar ♦♦ 20
0
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216
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... 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
spriyansh29 • 30
0
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1
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216
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1
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... 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
spriyansh29 • 30
Latest awards to spriyansh29
Student
6 months ago,
asked a question with at least 3 up-votes.
For Identification of Human Genes ?
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