User: Santosh Anand

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Santosh Anand3.2k
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Posts by Santosh Anand

<prev • 509 results • page 1 of 51 • next >
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Comment: C: Read counts of STAR with gff file
... Can you check by removing the option `--sjdbGTFfile gff` ? This option defines the path of GTF file, and since there is no gtf-file in the current dir named "gff", STAR might be not be doing anything. ...
written 4 hours ago by Santosh Anand3.2k
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Comment: C: Sub_sampling Paired_end reads in Fastq.gz format.
... Where is the link to your last post? Your questions are not very clear to me. But if you are interested in downsampling paired-end fasta, you may try `seqtk sample` command https://github.com/lh3/seqtk ...
written 7 hours ago by Santosh Anand3.2k
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Answer: A: RNA-Seq workflows available/ make your own
... For RNAseq differential Exp http://www.bioconductor.org/packages/3.7/bioc/vignettes/DESeq2/inst/doc/DESeq2.html Anything RNAseq https://rnaseq.uoregon.edu/ ...
written 11 hours ago by Santosh Anand3.2k
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Comment: C: How to show the entire query sequence in the alignment in NCBI stand-alone blast
... Blast is a local alignment tool. Maybe you are looking for a global aligner. See my answer in this post https://www.biostars.org/p/292003/ ...
written 1 day ago by Santosh Anand3.2k
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Answer: A: Should I use a bad/ mediocre gene model as input for STAR RNA-seq alignment?
... Q1: Gene-model is used only as a guide - not as an obligatory anchor. So, if you have a reasonable gene-model, even partial or incomplete, you should use it. Q2: IMO, 2-pass should be sufficient Q3a: For the same project, it is recommended because in this way, you have a pool of putative junction ...
written 1 day ago by Santosh Anand3.2k
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Comment: C: Penalty model of BWA MEM and BOWTIE2?
... > Are Gap open penalty in bowtie2 and bwa-mem meant to be same (in terms of value)? Do you compare the ripeness of bananas and oranges by comparing their colors, because both are fruits? BWA-mem and bowtei2 are different algorithms, and for sure there will be differences in how the gap penalty ...
written 1 day ago by Santosh Anand3.2k
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Comment: C: Penalty model of BWA MEM and BOWTIE2?
... Is it only me who is surprised that we are discussing whether BWA-mem is published and peer-reviewed or not? It looks absolutely ironical given the usage of BWA-mem in the early years before the explosion in the numbers of different kind of aligners, and not to discount the fact that there are still ...
written 1 day ago by Santosh Anand3.2k
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Comment: C: Penalty model of BWA MEM and BOWTIE2?
... Searcing for the word "penalty" in the respective manuals gives you all the details http://bio-bwa.sourceforge.net/bwa.shtml http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml ...
written 1 day ago by Santosh Anand3.2k
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Comment: C: How to retrieve nucleotid sequence from gene ids of ncbis "gene" data base?
... Sorry, my bad! What I meant was to use Entrez Direct command line tools: https://www.ncbi.nlm.nih.gov/books/NBK179288/ You can make complicated queries using that and can chain queries where the results from one query are fed to the next one. See if that helps. Also a youtube video is here https:/ ...
written 1 day ago by Santosh Anand3.2k
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Comment: C: DESeq result "LFC > 0 (up) : 0, 0% ,LFC > 0 (down) : 0, 0%"
... Newer and faster alternative pipeline is to use transcript abundance quantification methods such as Salmon (Patro et al. 2017), Sailfish (Patro, Mount, and Kingsford 2014), kallisto (Bray et al. 2016), or RSEM (B. Li and Dewey 2011), to estimate abundances without aligning reads. Also see, https: ...
written 1 day ago by Santosh Anand3.2k

Latest awards to Santosh Anand

Teacher 1 day ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 1 day ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Commentator 12 days ago, created a comment with at least 3 up-votes. For C: Merge two BAM files with different but overlapping reference sequences?
Teacher 3 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 3 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 3 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: read.table does not read in all rows!
Scholar 4 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 4 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 4 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 5 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 5 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 5 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 6 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 6 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Merge two BAM files with different but overlapping reference sequences?
Scholar 6 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 6 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 6 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 6 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Scholar 7 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 7 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Voter 7 months ago, voted more than 100 times.
Scholar 8 months ago, created an answer that has been accepted. For C: Visualizing hg19 and hg38 FPKMs in a single plot
Teacher 8 months ago, created an answer with at least 3 up-votes. For C: Visualizing hg19 and hg38 FPKMs in a single plot

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