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15 results • Page
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Votes
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2
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6
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438
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which statistical test and which package for comapre datasets?
R
package
statistical
test
updated 11 hours ago by
LauferVA
3.8k • written 1 day ago by
satva72
• 0
0
votes
0
replies
72
views
Is there any s/w that can be used to map metabolite results to it's pathway/s?
R
metabolomics
proteomics
Python
17 hours ago by
WUSCHEL
▴ 740
0
votes
0
replies
62
views
Loss of 'var' using concatenation of AnnData objects
var
Scanpy
AnnData
Concatenation
16 hours ago by
Rachel
• 0
0
votes
0
replies
54
views
PacBio subreads.fastq files?
subreads.fastq
ncbi
PacBbio
9 hours ago by
majeedaasim
▴ 60
0
votes
0
replies
151
views
Extract upstream and downstream 50bp nontemplated sequences from a position
search
sequences
nontemplated
motif
8 hours ago by
Ty
• 0
0
votes
1
reply
176
views
bcftools=1.18 not filtering correcting MAF
bcftools
minor-allele-frequency
VCF
updated 6 hours ago by
raphael.B
▴ 470 • written 2 days ago by
AMARU
• 0
0
votes
1
reply
177
views
How to remove 3rd codon positions in a multiple sequence allignment?
iqtree
CODON5
charset
6 hours ago by
francesco.degiglio
• 0
0
votes
2
replies
92
views
How to cluster .faa files?
faa
protein
clustering
amino-acids
updated 5 hours ago by
dthorbur
▴ 890 • written 6 hours ago by
bioinformagician
• 0
0
votes
0
replies
39
views
How to input list into GenomicsDBImport with snakemake?
snakemake
GenomicsDBImport
GATK
VCF
4 hours ago by
ema
• 0
0
votes
2
replies
195
views
i ues schicexplorer's hicbuildmatrix code complains that two sam files do not have the same reads order
hicbuidmatrix
schic
4 hours ago by
1125195245
• 0
0
votes
0
replies
35
views
Condition specific marker detection and problem with the distribution of cells from different samples
scRNAseq
3 hours ago by
Sara
▴ 230
0
votes
0
replies
44
views
Need Help Mapping Probe IDs to Gene Symbols
microarray
3 hours ago by
maryam.kh
• 0
0
votes
0
replies
20
views
Calculate Jukes-Cantor, Kimura, Tamura-Nei etc distances from BAM files
Kimura
minimap2
samtools
biopython
pysam
1 hour ago by
James G
▴ 10
0
votes
2
replies
248
views
Alternative to Gentrome?
salmon
updated 17 hours ago by
cfos4698
▴ 920 • written 2 days ago by
yee
• 0
0
votes
4
replies
293
views
Is interleaved Fastq files the same as interlaced fastq
fastq
updated 32 minutes ago by
Ram
41k • written 2 days ago by
RCMC
• 0
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The Biostar Herald for Monday, December 11, 2023
Comment: GATK GetPileupSummaries Java heap space
The Biostar Herald for Monday, December 11, 2023
A: How To Sort Sam File
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Answer: Autocompleting paths within scripts
Are Variable Features ranked in seurat?
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Comment: How should I run ssgsea analysis ?
by
Ram
41k
Just add a statement to your comments stating that the text was generated using ChatGPT - it is a good tool but it's not aware of its own s…
Comment: Autocompleting paths within scripts
by
DanielEB_fisk
▴ 20
Yep, sorry, you are right it is not a bioinformatics question. I asked here because it relates with the work we do anyway.
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41k
That section is for after you have virtualbox set up. You may have to run a really old version of macOS within the virtualbox, so be prepar…
Comment: ChatGPT optimized for bioinformatics questions
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Ram
41k
I understand. The purpose of my comment is to serve as feedback.
Comment: How can I obtain the DNA sequences of each CDS for several genbank files?
by
Ram
41k
Look into passing command line parameters to a python script. You can pass the input file name as a parameter to the script and execute the…
Answer: Autocompleting paths within scripts
by
Michael
53k
Not really a Bioinformatics question but generally very useful: [vim can do that][1] [type some prefix of path]<Ctrl-x><Ctrl-f> This…
Comment: How can I obtain the DNA sequences of each CDS for several genbank files?
by
Raphaëlle
• 0
Hello, Thank you very much for your quick reply. That was indeed the issue! Another question: is there a simple way of automating this …
Answer: Cluster sub-set analysis using Seurat
by
j.gleixner
▴ 10
There now is also `Seurat::FindSubCluster`
Comment: How can i control the cluster number in scRNASeq clustering by Seurat package
by
j.gleixner
▴ 10
There is now also Seurat::BuildClusterTree that makes this easier.
Answer: How can i control the cluster number in scRNASeq clustering by Seurat package
by
j.gleixner
▴ 10
If you want to get a certain number of clusters without resorting to trying different settings for the resolution parameter, you can firs…
Answer: How to speed-up to contruct phylogenetic tree
by
Nelo
▴ 20
I will also try this `fasttree`
Comment: i ues schicexplorer's hicbuildmatrix code complains that two sam files do not ha
by
1125195245
• 0
I tried using bowtie2's --reorder command to output a sam file for each of the two files, and then used both sam files to build the matrix,…
Comment: How to speed-up to contruct phylogenetic tree
by
Nelo
▴ 20
I used MEGA CC (comand line option) but there is no option to specify threads in its `--help` manual . And default thread is 4
Comment: How to speed-up to contruct phylogenetic tree
by
Nelo
▴ 20
The average length of fasta sequences is ~300aa length. I can't exclude any sequences as I have to provide them nomenclature aslo on the ba…
Comment: How to speed-up to contruct phylogenetic tree
by
Nelo
▴ 20
I used Raxml for a trial fasta file of about only 33 sequences as: `raxmlHPC-PTHREADS-AVX -f a -T 80 -m PROTGAMMAWAG -n test1 -s bittergou…
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