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Comment: downloading chemical database from ChEMBL
Seurat-Merging and integrate
voom mean-variance plot has set of genes where variance increases with expression level
Answer: vg autoindex seems stuck after a week of running
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
Answer: DESeq2 single cell pseudobulk
Comment: error when installing gistic2 using conda
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Recent Replies
Comment: from CRAM to fastq
by
ATpoint
82k
I am 99.99 sure that your fastq file is not compressed. What is `fileC-7507T.fastq.gz`? I do not think samtools autodetects suffix if you s…
Comment: from CRAM to fastq
by
GenoMax
142k
Possibly. You appear to have written the data to a single file (in case it was paired-end to begin with). Check to make sure secondary alig…
Comment: converting transcript IDs (Ensembl) to gene symbols in R
by
GenoMax
142k
https://www.biostars.org/u/18990/ : Please do not delete threads that have received a comment/answer.
Comment: downloading chemical database from ChEMBL
by
GenoMax
142k
Activities with `cucurbitacin A`: https://www.ebi.ac.uk/chembl/web_components/explore/activities/STATE_ID:RHxG8uDfrtbmiyaY55ic-w%3D%3D `cu…
Comment: KEGG analysis in R
by
letizia.ottaviani
• 0
Hello, I have a problem to do the analysis in R. I want to kindly ask you: How did you perform KEGG pathway enrichment analysis in R for…
Comment: downloading chemical database from ChEMBL
by
s
• 0
Thank you for your reply. I am still struggling with the first step, namely "select a compound" . can you be more specific with this step? …
Comment: No output when converting transcript IDs to gene symbols
by
ATpoint
82k
Honestly, why the overhead with biomart? Get a GTF file that matches your annotations, and just do a left join with your transcript IDs, it…
Answer: vg autoindex seems stuck after a week of running
by
Jouni Sirén
▴ 370
GCSA construction is fragile. It can use effectively unlimited amounts of time, memory, and disk space if the graph is too complex. That's …
Comment: Blastn, need help to increase speed
by
Dunois
★ 2.5k
What databases are you using that are creating such large index files?
Answer: Kraken2 Custom Database non-deterministic results
by
colindaven
6.4k
You're using 2 different databases, so results are obviously different. This has nothing to do with deterministic or stochastic behaviour. …
Answer: How to get 2 seurat objects into a DEseq
by
ultraanfibio
▴ 30
Its probably best practice to read all samples into the same seurat object, then do the clustering and asign the cell type labels. Anyways …
Comment: How do we do quantification using stringtie merge option for all the merged samp
by
ATpoint
82k
I ask the same I always ask when people use stringtie for human data. Do you really need a transcript assembly or do you just want gene cou…
Comment: Mapping difference with BWA
by
ATpoint
82k
Cannot be answered without more details. At least add accessions and commands.
Comment: vcf phasing
by
safeassli
▴ 10
Sprry but I'm not an expert in this field. I'm trying to learn Only 0/1, 1/0, and 1/1 genotypes should be phased, as these indicate the pr…
Comment: z-score of gene set
by
Hien
• 0
I have a list of genes in some pathways, I want to see these pathways which are upregulated or downregulated in a total of gene expressions…
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