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bharata1803
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Mensur Dlakic
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Recent Replies
Comment: Bacterial Pangenome Analysis
by
kirankumareripogu
▴
10
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
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
•
0
Works with `useMart(biomart="fungi_mart", dataset="spombe_eg_gene", host="https://fungi.ensembl.org")`
Comment: Bug of vg surject
by
Jordan M Eizenga
▴
360
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?
by
Chris
▴
180
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
by
Qi
•
0
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
by
Jordan M Eizenga
▴
360
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?
by
Yogi
▴
20
Few things to mention.
Pathway Enrichment Analysis can be split into two categories.
1. Functional Class Scoring Methods
2. Overrepr…
Answer: identify DEGs across all conditions and per specific conditions
by
Yogi
▴
20
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
by
Istvan Albert
98k
yes correct you have to pass the full prefix and not the directory
Comment: Low Alignment rate
by
dsull
★
4.7k
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…
Comment: Troubles launch IGV on Linux(Debian)
by
morovatunc
▴
550
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…
Comment: How to check RNAseq support for annotated genes?
by
Michael
53k
> 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
by
Ram
40k
The error message tells me there is the possibility of a conflicting function called `plot_genes_violin` that accepts one parameter and err…
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