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Comment: Problem in getting geo file through GEOQUERY
Answer: Question about samtools view flags (paired reads vs. properly paired reads)
Answer: Functional enrichment analysis for unique gene IDs
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Comment: Why does assigning genes with biomart give me different values than using a tran
Comment: Multiplexing for pooled CRISPR screen sequencing
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
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Recent Replies
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
shpak.max
▴ 50
If that were the case, I would expect there not to be any uncalled sites in the vcf, yet there are a large number of sites with "." placeho…
Comment: Problem in getting geo file through GEOQUERY
by
bk11
★ 2.5k
It just runs fine for me with just a single line of code. library(GEOquery) GSE1145 <- getGEO("GSE1145", GSEMatrix=TRUE) …
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
Dave Carlson
★ 1.7k
I can't speak to UnifiedGenotyper, as it has been many years since GATK stopped supporting it, and I have not used it in a long time. But …
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
I want to get lot of files through code
Comment: Problem in getting geo file through GEOQUERY
by
GenoMax
142k
Query seems to be timing out. Try getting the file directly here: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1145/matrix/GSE1145-GP…
Comment: Add stats to the plot
by
Ghada
• 0
Thanks for the help. Unfortunately, did not work :( error in asserttat_group_columns_exists(data) : data should contain group1 and grou…
Comment: downloading chemical database from ChEMBL
by
GenoMax
142k
How about following https://www.ebi.ac.uk/chembl/web_components/explore/activities/ --> Select a compound --> Related Targets button --> D…
Comment: Genotyping sites with N in reference genome
by
shpak.max
▴ 50
As a follow-up, is it possible to get a variant call with UnifiedGenotyper if rather than N, I have one of the ambiguity codes (e.g. R, Y, …
Answer: Allele count of 2 for homoplasmic MT variants in VCF
by
LChart
3.9k
The GATK (and afaik every caller that I know) treats every contig of the reference as having the same ploidy (so all haploid, all diploid, …
Comment: Where are the illumina adapters on Trimmomatic take from?
by
GenoMax
142k
Use the sequence Illumina recommends for the specific kit.
Comment: Question about samtools view flags (paired reads vs. properly paired reads)
by
Pierre Lindenbaum
161k
> Thanks. What determines what constitutes a good distance? I think tools like BWA use the median distance for each chunk of processed d…
Comment: Where are the illumina adapters on Trimmomatic take from?
by
bioinfo
▴ 150
Thank you for the explanation. Is it more appropriate then to use the sequence from the illumina documentation or the one from the github?
Comment: Question about samtools view flags (paired reads vs. properly paired reads)
by
mrk
• 0
Thanks. What determines what constitutes a good distance? I have some targeted panel data and looking at flagstat, almost all reads are pai…
Answer: Where are the illumina adapters on Trimmomatic take from?
by
GenoMax
142k
Illumina indexed adapters share a core sequence at the beginning which is what is indicated in your link. Trimming programs will remove seq…
Comment: Allele count of 2 for homoplasmic MT variants in VCF
by
Ram
44k
Please stop using `bioinformatics` as a tag unless your post is about the field of bioinformatics itself.
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