User: Prakash

gravatar for Prakash
Prakash1.9k
Reputation:
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Location:
India
Twitter:
gprakash047
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Google Scholar Page
Last seen:
3 days ago
Joined:
4 years, 12 months ago
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Posts by Prakash

<prev • 148 results • page 1 of 15 • next >
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Comment: C: BWA mem and Samtools sort in Bash script
... Thanks [WoterDeCoster][1] for this information [1]: https://www.biostars.org/u/24526/ ...
written 20 days ago by Prakash1.9k
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Comment: A: BWA mem and Samtools sort in Bash script
... I think you need to also add `-O BAM` argument to write the output to file ...
written 20 days ago by Prakash1.9k
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Comment: C: Unable to locate libraries in latest version of R 4.0.0
... Recently I had similar issue, then I had to recompile everything. I just took the list of packages from the existing library. Here you can use your own library path pkgs <- rownames(installed.packages(lib.loc = "/Users/mtoufiq/Library/R/3.5/library")) and compile everything as suggested by ...
written 10 weeks ago by Prakash1.9k
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Answer: A: GoProfiler compareGeneLists Error
... I tried to reproduce your problem, however, in my case, I didn' get the error that you encountered. Here is the output that I got > print(gene1Compared) $MF linear combination of chi-squares statistic data: expanded1[[i]] and expanded2[[i]] and NULL (n*m/(n+m)) * ...
written 10 weeks ago by Prakash1.9k
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Comment: C: error in reorder the bars of ggplots
... x =reorder(Term, -logPValue) should work ...
written 12 weeks ago by Prakash1.9k
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Comment: C: Changing distance to TSS (tssRegion in ChIPseeker) during peak annotation in ChI
... The basic principle for ChIP-seq peaks annotation is to identify the nearest TSS (genes). so even though you increase the range of window upstream or downstream of TSS the number of annotated genes will remain constant. But In case you increase it to 10000, one peak might be annotated to several ge ...
written 3 months ago by Prakash1.9k
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Comment: C: GSEA/fold change for ChIP-seq
... Apart from peak calling and annotation, ChIPseq data can also be used to find differential genomic regions across conditions. [DiffBind][1] performs such kind of analysis that internally uses [DESeq2][2] for differential analysis. Similar to raw count for genes, Diffbind extracts raw counts for geno ...
written 4 months ago by Prakash1.9k
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Comment: C: bedGraphToBigWig file converter
... This GitHub post might be helpful for you. https://github.com/taoliu/MACS/wiki/Build-Signal-Track ...
written 4 months ago by Prakash1.9k
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Comment: C: How to cat fastq files but keep different samples separate
... I agree with you [ATpoint][1], paired-end data R1 and R2 should be kept separate. Thanks for highlighting this point. Few things are still no clear to me such as > no overlap between forward and reverse reads > merged reads are not required also as Joe highlighted > difference between ...
written 4 months ago by Prakash1.9k
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Answer: A: How to cat fastq files but keep different samples separate
... $f used in output will create output for each line. you need to try : for f in Sample1_C*.fastq.gz; do cat $f > Sample1_C_merged.fastq.gz; done for f in Sample1_L*.fastq.gz; do cat $f > Sample1_L_merged.fastq.gz; done ...
written 4 months ago by Prakash1.9k

Latest awards to Prakash

Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Error while running computeMatrix of deepTools
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Voter 4 months ago, voted more than 100 times.
Student 6 months ago, asked a question with at least 3 up-votes. For Motif analysis from H3K27ac ChIPseq broad peaks
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Delete numbers in the tables column
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Appreciated 10 months ago, created a post with more than 5 votes. For A: How to add colors to bar chart?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Popular Question 10 months ago, created a question with more than 1,000 views. For Error while running computeMatrix of deepTools
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Appreciated 11 months ago, created a post with more than 5 votes. For A: Delete numbers in the tables column
Appreciated 11 months ago, created a post with more than 5 votes. For A: How to add colors to bar chart?
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: How to add gene symbol to RNA-Seq data using R
Appreciated 12 months ago, created a post with more than 5 votes. For A: How to add colors to bar chart?
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: How to add gene symbol to RNA-Seq data using R
Scholar 12 months ago, created an answer that has been accepted. For A: How to add colors to bar chart?
Appreciated 12 months ago, created a post with more than 5 votes. For A: How to add colors to bar chart?
Scholar 13 months ago, created an answer that has been accepted. For A: How to add colors to bar chart?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Delete numbers in the tables column
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?

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