User: khorms
khorms • 110
- Reputation:
- 110
- Status:
- Trusted
- Location:
- Moscow
- Last seen:
- 22 hours ago
- Joined:
- 6 years, 11 months ago
- Email:
- k*******@gmail.com
about me
Posts by khorms
<prev
• 38 results •
page 1 of 4 •
next >
1
vote
1
answer
61
views
1
answers
... An easy way of doing it is to run samtools flagstat on multiple .bam files and then combine their output together using [multiqc][1]
So something like
samtools_stat_commands=()
samtools_stat_log_folder=''
multiqc_folder=''
for i in ${aligned_folder}/*.bam
do
sample_name=$(basename $ ...
written 12 days ago by
khorms • 110
2
votes
3
answers
99
views
3
answers
... I don't think there are any. In order to double check, you could do this:
This [table][1] show the codes for sample types; so all you need to know to figure out what kind of sample you are looking at is the last two digit barcode.
You could go to [Xena][2], look at the pages corresponding to the ...
written 14 days ago by
khorms • 110
0
votes
1
answer
54
views
1
answers
... You could use [IGV][1] to visualize both your alignment .bam file and your bed file; this way you could manually inspect the regions of interest
[1]: http://software.broadinstitute.org/software/igv/ ...
written 14 days ago by
khorms • 110
0
votes
1
answer
66
views
1
answers
... pysam pileup chooses all the reads that align to the selected region, then iterates through all the positions covered by these reads. Therefore, it's expected that the value you get in the end for counter is larger than 100 (since some reads extend beyond the region you have specified). I am not sur ...
written 15 days ago by
khorms • 110
0
votes
0
answers
71
views
0
answers
... A question to the folks who studies Alzheimer's disease here.
My colleagues and I have developed a new program that predicts the master regulators based on transcriptomic changes (yes, another one). We have applied it to Alzheimer's disease RNAseq datasets and we have identified several potential m ...
0
votes
0
answers
108
views
0
answers
... Are you talking about the initial preprocessing (like 10X's CellRanger) or downstream analysis? Which tool did you use that didn't like the 64G limit? I know that CellRanger by default tries to use 90% of all memory on the machine and therefore causes troubles; you have to explicitly specify the amo ...
written 16 days ago by
khorms • 110
1
vote
1
answer
106
views
1
answers
... I am not sure about Seurat but another very popular single cell analysis framework Scanpy allows you do perform GSVA analysis with tools like [diffxpy][1]
[1]: https://diffxpy.readthedocs.io/en/latest/api/index.html#gene-set-enrichment-enrich ...
written 16 days ago by
khorms • 110
0
votes
2
answers
73
views
2
answers
... Can't you just download biomaRt tables and use them to look up the correspondence like it's done [here][1]?
[1]: https://stackoverflow.com/questions/53339481/entrez-gene-ids-from-gene-list-using-biomart ...
written 19 days ago by
khorms • 110
2
votes
1
answer
98
views
1
answers
... In the Ensembl link you attached, there are files that are named something-something-"assembly", for example Mus_musculus.GRCm38.dna.primary_assembly - that is what you need ...
written 19 days ago by
khorms • 110
0
votes
0
answers
204
views
0
answers
... The authors say in the Methods section that they used CellRanger to process their sequencing reads. Is there any particular reason (bseides speed) why you are using Salmon? As far as I know it's a standard practice to use CellRanger software when working with 10X data, and I wouldn't always expect S ...
written 10 weeks ago by
khorms • 110
Latest awards to khorms
Scholar
19 days ago,
created an answer that has been accepted.
For A: How to generate a mouse reference genome in STAR?
Popular Question
2.8 years ago,
created a question with more than 1,000 views.
For How to avoid a phylogenetic bias testing a hypothesis on a big set of bacterial genomes
Popular Question
2.8 years ago,
created a question with more than 1,000 views.
For Getting upstream of a given gene from a .gbk file
Popular Question
2.8 years ago,
created a question with more than 1,000 views.
For Downloading genes annotations from UCSC Table Browser
Popular Question
2.8 years ago,
created a question with more than 1,000 views.
For Visualisation of clusters produced by mothur
Popular Question
2.8 years ago,
created a question with more than 1,000 views.
For How to get the abundance of genes in metagenomes from MG RAST
Popular Question
3.3 years ago,
created a question with more than 1,000 views.
For How to get the abundance of genes in metagenomes from MG RAST
Popular Question
4.2 years ago,
created a question with more than 1,000 views.
For getting data from american gut project
Popular Question
5.5 years ago,
created a question with more than 1,000 views.
For How to get the abundance of genes in metagenomes from MG RAST
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1588 users visited in the last hour