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Scholar to
Pierre Lindenbaum
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deniselavezzari
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Rafael Soler
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realnewbie
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Recent Replies
Answer: How to subset a GVCF using GATK SelectVariants
by
Pierre Lindenbaum
146k
https://gatk.broadinstitute.org/hc/en-us/articles/360037055952-SelectVariants#--sample-name
> --sample-name / -sn
> This argument c…
Comment: How to subset a GVCF using GATK SelectVariants
by
Pierre Lindenbaum
146k
are you sure it's safe reduce the number of samples from a g.vcf file (!= vcf) ?
Comment: Multiple exposure timelines (time-points) in one DESeq2 object or multiple DESeq
by
Rafael Soler
▴
430
Oh, I see. Thank you :)
Comment: Convert a BAM from GRCh37 to hg19?
by
Giovanni M Dall'Olio
27k
Thanks for sharing the solution!
Comment: Statistical test for RNAseq Clustering
by
HERMAN
•
0
Thank you very much for your reply ! I will try to discuss this with my biologist colleagues
Comment: Multiple exposure timelines (time-points) in one DESeq2 object or multiple DESeq
by
ATpoint
62k
+1, fyi you can simply post a plain biostars link to an existing thread/answer, it will then display the title of the thread, there is no n…
Comment: Convert a BAM from GRCh37 to hg19?
by
GenoMax
117k
While major genome builds are identical there are specific differences in non-chromosomal members: https://gatk.broadinstitute.org/hc/en-us…
Answer: Convert a BAM from GRCh37 to hg19?
by
Joel Wallenius
▴
100
I ended up using samtools reheader, as the chromosomes seemed similar enough. I ended up wasting some hours thinking reheader ONLY changed …
Comment: PLINK CASE-CONTROL ANALYSIS
by
Nai
▴
20
Dear Pierre,
Sorry, I would like to perform in Plink. The question is to generate .bed, .map. .fim files from csv files having Marker, var…
Answer: gene library composition
by
Rafael Soler
▴
430
Hello!
You can put these genes in websites like [DAVID][1], [REACTOME][2], or [PANTHER][3] to classify them according to their functions…
Comment: Validate mutations from WGS using RNA-seq bam files in IGV?
by
Arup Ghosh
2.9k
The authors have mentioned using two approaches for validation. Although they have not mentioned the exact criteria for the RNA-seq based a…
Answer: Multiple exposure timelines (time-points) in one DESeq2 object or multiple DESeq
by
Rafael Soler
▴
430
The dispersion estimates will change depending on whether you analyze the data together or separately, so the best strategy depends on the …
Answer: Extract all regions in a genome that are not assembly gaps from a FASTA file qui
by
Ivan
▴
50
What Pierre Lindenbaum posted works, but I couldn't be bothered to install another software to my space.
The stuff I wrote in Python was v…
Comment: Overlapping regions in a BED file
by
GenoMax
117k
They are standard feature types (describing gene and its products) that are defined in GTF/GFF files from which your BED file is likely der…
Answer: Hands-On RNA-Seq Data Analysis Workshop in Leipzig, Germany (October 25-28, 2022
by
David Langenberger
9.7k
**Update**: If there are limitations on the number of participants due to rising Covid 19 cases, priority will be given to those who have r…
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