Moderator: b.nota

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b.nota6.0k
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Posts by b.nota

<prev • 897 results • page 1 of 90 • next >
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Comment: C: Is possible to recreate RNASeq count dataset from a dataset normalized with FPKM
... Unfortunately, it is not possible to calculate raw counts from RPKM data. Best is to start with bam files, and use a program such as `featureCounts` to generate raw counts. ...
written 18 hours ago by b.nota6.0k
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Comment: C: bwa: fail to locate the index files
... Nice, you can upvote (thumb up) an answer that was useful, or even accept that answer. ...
written 21 hours ago by b.nota6.0k
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Comment: C: bwa: fail to locate the index files
... Did you try `myref.fasta` instead of just `myref`? ...
written 1 day ago by b.nota6.0k
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Comment: C: The 2013 Eisenberg and Levanon housekeeping genes list for Human is the most upd
... Thanks for adding the extra information. ...
written 1 day ago by b.nota6.0k
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Comment: C: Housekeeping genes list for Human
... What kind of analysis? Did you searched literature already? ...
written 1 day ago by b.nota6.0k
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Answer: A: How to get number of exons for each transcript in biomart
... I wouldn't use `biomaRt`, but try to use `AWK` instead. If you download the annotation `gtf` file from [ensemble][1], you can try something like this with `AWK`: awk '$3=="exon" {print $0}' Homo_sapiens.GRCh38.78.gtf | awk '{ count[$10]++ } END { for (word in count) print word, count[word]}' &g ...
written 2 days ago by b.nota6.0k
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Comment: C: Bash and seqret problem
... You can try to put it in a [for][1] loop. [1]: https://www.cyberciti.biz/faq/bash-for-loop/ ...
written 2 days ago by b.nota6.0k
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Comment: C: What are alleles Y, Z
... Maybe [this][1] can help here. So an insertion of T or C is my interpretation. [1]: https://en.wikipedia.org/wiki/Nucleic_acid_notation ...
written 3 days ago by b.nota6.0k
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Comment: C: PhD Student Position in Genetics (bioinformatics)
... Is Wageningen Germany? ...
written 3 days ago by b.nota6.0k
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Answer: C: can we replace #N/a with 0 for using edgeR
... edgeR is not suitable for analysis with FPKM, see [user's guide][1] section 2.3 on page 12. > Note that edgeR is designed to work with actual read counts. We not > recommend that predicted transcript abundances are input the edgeR in > place of actual counts. [1]: https://bioconductor ...
written 3 days ago by b.nota6.0k

Latest awards to b.nota

Great Question 10 days ago, created a question with more than 5,000 views. For heatmap.2 reorder branches
Popular Question 18 days ago, created a question with more than 1,000 views. For phred 33 from Ion S5?
Commentator 23 days ago, created a comment with at least 3 up-votes. For C: RNA to protein in bash?
Scholar 24 days ago, created an answer that has been accepted. For C: Find genes of enriched known motif results in HOMER
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: trimming the paired end reads with cutadapt
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: RNA to protein in bash?
Scholar 4 weeks ago, created an answer that has been accepted. For C: Find genes of enriched known motif results in HOMER
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: trimming the paired end reads with cutadapt
Scholar 5 weeks ago, created an answer that has been accepted. For C: Find genes of enriched known motif results in HOMER
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: RNA to protein in bash?
Popular Question 9 weeks ago, created a question with more than 1,000 views. For phred 33 from Ion S5?
Scholar 11 weeks ago, created an answer that has been accepted. For C: Find genes of enriched known motif results in HOMER
Appreciated 3 months ago, created a post with more than 5 votes. For A: Bioinformatics freelancers needed
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: RNA to protein in bash?
Appreciated 3 months ago, created a post with more than 5 votes. For A: Bioinformatics freelancers needed
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics freelancers needed
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: trimming the paired end reads with cutadapt
Popular Question 3 months ago, created a question with more than 1,000 views. For phred 33 from Ion S5?
Scholar 4 months ago, created an answer that has been accepted. For C: Find genes of enriched known motif results in HOMER
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: trimming the paired end reads with cutadapt
Scholar 4 months ago, created an answer that has been accepted. For C: Find genes of enriched known motif results in HOMER
Popular Question 5 months ago, created a question with more than 1,000 views. For RNAseq analysis with Ion AmpliSeq Transcriptome Solution data
Popular Question 5 months ago, created a question with more than 1,000 views. For RNAseq analysis with Ion AmpliSeq Transcriptome Solution data
Appreciated 5 months ago, created a post with more than 5 votes. For A: Bioinformatics freelancers needed
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: trimming the paired end reads with cutadapt

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