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Recent Replies
Answer: Fetch Fastq files directly for SRA data
by
Rob
6.2k
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
by
YUYANG.OON
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Works with `useMart(biomart="fungi_mart", dataset="spombe_eg_gene", host="https://fungi.ensembl.org")`
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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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Chris
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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
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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…
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Few things to mention.
Pathway Enrichment Analysis can be split into two categories.
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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…
Comment: Hisat2 index and alignment question
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Istvan Albert
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yes correct you have to pass the full prefix and not the directory
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dsull
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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
by
Mehwish
•
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 …
Comment: Violin plot (Monocle 3) - Troubleshooting
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The error message tells me there is the possibility of a conflicting function called `plot_genes_violin` that accepts one parameter and err…
Comment: Violin plot (Monocle 3) - Troubleshooting
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bk11
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I m not sure why you have problem there. I do not encounter any problem. May be your gene list are not present in your source object. Pleas…
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