User: steve

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Posts by steve

<prev • 168 results • page 1 of 17 • next >
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Comment: C: VCF file manipulation for extracting the required information
... you can also probably get this from annotating with ANNOVAR or similar. ...
written 1 day ago by steve1.4k
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Comment: C: 5 FAsta file input and showing result using nested loop
... This sounds like someone's homework assignment. ...
written 4 days ago by steve1.4k
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Comment: C: Changing the legend names: R
... Another thing you might consider is making a copy of the 'Condition' column in your dataframe, converting it to Factor, then changing the 'levels' of the factor to "condition1", "condition2", etc.. This way, all the entries are still part of the same groupings, but those groups have the desired name ...
written 4 days ago by steve1.4k
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Comment: C: Survey: help define Gencode and NCBI primary transcripts
... maybe relevant post here: https://www.biostars.org/p/209633/ ...
written 9 days ago by steve1.4k
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Comment: C: HISAT2 for loop shell scripting
... Do not use quotes with shell globs (aka `*`); the command needs to be: `ls *.fastq` ...
written 14 days ago by steve1.4k
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Comment: C: HISAT2 for loop shell scripting
... can you update your original post with the modified code you are using, and any error message you are getting? Also can you give the `ls` or `tree` output of the directory you are running the script in? ...
written 14 days ago by steve1.4k
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Answer: A: Problems left-normalizing variants with bctools, GATK, combining with ANNOVAR an
... It looks like a lot of my problems were solved by using the `--vcfinput` option of ANNOVAR, among other things, like this: table_annovar.pl "${sample_vcf}" "${annovar_db_dir}" \ --buildver "${params.ANNOVAR_BUILD_VERSION}" \ --remove \ --protocol "${params.AN ...
written 16 days ago by steve1.4k
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Comment: C: Problems left-normalizing variants with bctools, GATK, combining with ANNOVAR an
... In this case, I need to recalculate the allele frequencies from GATK HaplotypeCaller, since they are not listed as the empirical values, and I want to propagate that value through to the final annotation table. ...
written 16 days ago by steve1.4k
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Problems left-normalizing variants with bctools, GATK, combining with ANNOVAR annotations
... I am trying to normalize, filter, and annotate variants in .vcf format. Right now, my workflow looks like this: - left-normalize & filter .vcf (bcftools / GATK) - convert .vcf to .tsv (GATK) - recalculate values in .tsv (e.g. `HaplotypeCaller` frequency, etc.) - annotate .vcf (ANNOVAR) ...
annotation variant written 16 days ago by steve1.4k
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Comment: C: Creating Interactive Volcano Plots with R and Plot.ly
... what exactly is the problem? Can you update the post to include the exact code you are running & the error message? ...
written 16 days ago by steve1.4k

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Popular Question 26 days ago, created a question with more than 1,000 views. For HOMER mergePeaks totals don't add up to peaks input
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Visualization of Homer mergePeaks output Venn?
Epic Question 6 weeks ago, created a question with more than 10,000 views. For Creating Interactive Volcano Plots with R and Plot.ly
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Popular Question 7 weeks ago, created a question with more than 1,000 views. For HOMER mergePeaks totals don't add up to peaks input
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
Scholar 11 weeks ago, created an answer that has been accepted. For A: HOMER mergePeaks totals don't add up to peaks input
Popular Question 3 months ago, created a question with more than 1,000 views. For How to tell which transcript is the canonical transcript?
Popular Question 4 months ago, created a question with more than 1,000 views. For How to tell which transcript is the canonical transcript?
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: StackExchange/Area51 bioinformatics is back
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Visualization of Homer mergePeaks output Venn?
Guru 5 months ago, received more than 100 upvotes.
Appreciated 5 months ago, created a post with more than 5 votes. For Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
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Great Question 8 months ago, created a question with more than 5,000 views. For Creating Interactive Volcano Plots with R and Plot.ly
Appreciated 8 months ago, created a post with more than 5 votes. For Automatic IGV snapshot script
Popular Question 9 months ago, created a question with more than 1,000 views. For How to tell which transcript is the canonical transcript?
Popular Question 10 months ago, created a question with more than 1,000 views. For Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: StackExchange/Area51 bioinformatics is back
Appreciated 12 months ago, created a post with more than 5 votes. For Automatic IGV snapshot script
Appreciated 13 months ago, created a post with more than 5 votes. For Automatic IGV snapshot script
Student 13 months ago, asked a question with at least 3 up-votes. For How to tell which transcript is the canonical transcript?
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Appreciated 19 months ago, created a post with more than 5 votes. For Creating Interactive Volcano Plots with R and Plot.ly

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