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Recent Replies
Comment: Which function is best for pathway analysis?
by
luffy
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@chris Please look into @Hamid Ghaedi's well documented [post][1] on ORA and GSEA, Or [this][2] documentation. Hope this helps.
[1]: ht…
Comment: Bacterial Pangenome Analysis
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kirankumareripogu
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Hi @liorglic,
Thank you for your prompt response.
I totally agree with you that different blastp cuttoffs provide different results and…
Answer: Fetch Fastq files directly for SRA data
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Rob
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What is the accession for the project? Many — though not all — of the projects present in the NCBI SRA are also hosted in the European Nuc…
Comment: Dataset's name in BioMart for S. pombe
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YUYANG.OON
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Works with `useMart(biomart="fungi_mart", dataset="spombe_eg_gene", host="https://fungi.ensembl.org")`
Comment: Bug of vg surject
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Jordan M Eizenga
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This is still hard to interpret without the commands. What would help is if you literally copied the full UNIX commands along with their re…
Comment: Which function is best for pathway analysis?
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Thank you for your reply! Do you have code that I and others can implement? I am not sure how to customize the gmt file from my differentia…
Comment: Bug of vg surject
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Qi
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Thanks your reply!
my resulte show below:
5x_pan_sv.bam 1347587601 #converted from gam to bam F1 indel=0.830392 snp=0.932511
5…
Comment: Bug of vg surject
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It might help us to diagnose the problem if you included the exact commands that you used and showed the results that you are concerned abo…
Answer: Which function is best for pathway analysis?
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Yogi
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Few things to mention.
Pathway Enrichment Analysis can be split into two categories.
1. Functional Class Scoring Methods
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Answer: identify DEGs across all conditions and per specific conditions
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Yogi
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Couple of things.
(Feel free to correct if I'm misunderstanding).
"DESeq2" is meant for 1v1 comparisons.
If you're trying to compar…
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yes correct you have to pass the full prefix and not the directory
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Wow! Didn't realize the repeat-masked file could have such a large influence on alignment. Very good to know -- I guess I'll need to dive i…
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Disclaimer: My comment could be totally unrelated. I would give these a try if you have noone comment/answer your problem.
I have had this…
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> I tried it using STAR to map the transcript to the annotation gtf file
That is not what STAR is for. STAR is for aligning short reads in…
Comment: Low Alignment rate
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Mehwish
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0
Thanks alot! This worked out for me https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz …
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