User: ag1805x

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ag1805x80
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India
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https://ag1805x.github...
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1 day, 3 hours ago
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2 years, 7 months ago
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Posts by ag1805x

<prev • 90 results • page 1 of 9 • next >
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Answer: A: Run htseq-count with multiple sam files?
... A small perl script will do the job and then use R to combine results into one file. ...
written 14 days ago by ag1805x80
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Answer: A: htseq-counts output merge into one matrix ??
... I managed to do this by R. The script is available [here][1]. It works for me. Please try and check if it works fine. [1]: https://github.com/ag1805x/RNA-seq-analysis/blob/master/htseq-count_merge.R ...
written 14 days ago by ag1805x80
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Comment: C: How many genes in RNA seq?
... The overall alignment rate was >90% for all sample ...
written 14 days ago by ag1805x80
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Comment: C: How many genes in RNA seq?
... Actually I wanted to know this because DESeq2 gave me 18k DEG of all 60k. Does the total number matter in statistical analysis? ...
written 15 days ago by ag1805x80
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Comment: C: How many genes in RNA seq?
... Haven't touched novel transcripts yet. Looking to find DEG among known. The problem is DESeq2 reports ~18k DEG and Ballgown ~900 at p<0.05. ...
written 15 days ago by ag1805x80
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Comment: C: How many genes in RNA seq?
... Well 20K is protein coding genes. 60k includes pseudo genes and non-coding genes. Please refer http://mar2016.archive.ensembl.org/Homo_sapiens/Info/Annotation ...
written 15 days ago by ag1805x80
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How many genes in RNA seq?
... After running Stringtie/Feature counts the output is expression value of all the genes present in the annotation file. To be specific 60675 in GRCh38p5. For finding deferentially expressed genes is it good to work with all the genes? Are there any chance of duplicate genes in the number? There are ...
stringtie rna-seq written 15 days ago by ag1805x80
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Comment: C: Which HTSeq mode is suitable for RNAseq data to be used for differential gene ex
... Why? Any explanation for not prefering HTSeq. ...
written 29 days ago by ag1805x80
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Which HTSeq mode is suitable for RNAseq data to be used for differential gene expression?
... Which of the three modes -- union, intersection-strict, intersection-nonempty-- is suitable for RNAseq data to be used for differential gene expression? ...
ngs alignment rna-seq written 29 days ago by ag1805x80 • updated 29 days ago by h.mon15k
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What is a good Trimmomatic parameter?
... I am trying to clean RNAseq reads with TRIMMOMATIC using the parameters as: java -jar trimmomatic-0.36.jar PE -trimlog file_trim_log input_1.fastq.gz input_2.fastq.gz output_1P_clean.fq.gz output_1U_clean.fq.gz output_2P_clean.fq.gz output_2U_clean.fq.gz ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 SLI ...
trimmomatic ngs rna-seq sequencing written 5 weeks ago by ag1805x80

Latest awards to ag1805x

Popular Question 8 weeks ago, created a question with more than 1,000 views. For C program to find complementary of DNA sequence
Scholar 3 months ago, created an answer that has been accepted. For A: What is the difference between gene FPKM and transcript FPKM values?
Great Question 3 months ago, created a question with more than 5,000 views. For C program to find complementary of DNA sequence
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Popular Question 23 months ago, created a question with more than 1,000 views. For C program to find complementary of DNA sequence

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