User: deepak18

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deepak1810
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Posts by deepak18

<prev • 19 results • page 1 of 2 • next >
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How to make design and contrast matrix for microarray analysis using EventPointer?
... I am new to analysis of microarray data using R. I am using EventPointer package to analyze HTA 2.0 array data. Can someone elaborate on the design and contrast matrices that are required for this package to function? (https://bioconductor.org/packages/release/bioc/vignettes/EventPointer/inst/doc/Ev ...
microarray eventpointer written 10 months ago by deepak1810
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Comment: C: RNA-Seq Read Counting using featureCounts
... But then why STAR statistics tell a different story? Over 90% reads had mapped uniquely and only about 3% were muti-mapping. Number of input reads | 32604356 Average input read length | 300 UNIQUE READS: Uniqu ...
written 11 months ago by deepak1810
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Answer: A: RNA-Seq Read Counting using featureCounts
... Below is the results summary: #Without -O flag Assigned 4515031 Unassigned_Unmapped 0 Unassigned_Read_Type 0 Unassigned_Singleton 0 Unassigned_MappingQuality 0 Unassigned_Chimera 0 Unassigned_FragmentLength 0 Unassigned_Duplicate 0 Unassigned_MultiMapping 4898882 ...
written 11 months ago by deepak1810
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RNA-Seq Read Counting using featureCounts
... I am new to RNA-seq analysis of paired end read data and I was performing read counting using featureCounts. The use of -O flag increases the number of assigned reads drastically (difference of more than 20 million assigned reads). I don't quite understand the use of this option. In the manual it sa ...
featurecounts subread rna-seq written 11 months ago by deepak1810
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Comment: C: Problem during read counting with DEXSeq
... I was able to do it successfully with DEXSeq. The problem was the missing -r flag. Thanks for the valuable suggestions ...
written 11 months ago by deepak1810
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Comment: C: Problem during read counting with DEXSeq
... I repeated with Salmon. Indexing was done using transcriptome fasta file. I used the following code: #Generating Transcriptome Fasta file gffread -w Homo_sapiens_GRCh38.98.transcriptome.fa -g /home/erpl/RNA-seq_Alignment_tools/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa /home/erpl/RNA-seq_Al ...
written 11 months ago by deepak1810
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Comment: C: Problem during read counting with DEXSeq
... Over 90% uniquely mapped reads with all samples: Number of input reads | 32604356 Average input read length | 300 UNIQUE READS: Uniquely mapped reads number | 30430485 Uniquely mapped reads % ...
written 11 months ago by deepak1810
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Problem during read counting with DEXSeq
... I am currently trying to analyze RNA-seq data using DEXSeq. I am facing problem during the step where reads are counted. The output of read counting step generated a file which has very few transcripts which have count more than 0 (around 20,000). The output looks like this: ENSG00000000003:00 ...
dexseq rna-seq written 11 months ago by deepak1810
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Comment: C: DEXSeq Installation Error
... Yes installing libssl-dev worked. Thanks. ...
written 12 months ago by deepak1810
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Comment: A: DEXSeq Installation Error
... **What do I have to install outside of R? My OS is Ubuntu 19.04. After installing Anaconda2 I got this:** `------------------------- ANTICONF ERROR --------------------------- Configuration failed because openssl was not found. Try installing: * deb: libssl-dev (Debian, Ubuntu, etc) ...
written 12 months ago by deepak1810

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