User: lech.kaczmarczyk
lech.kaczmarczyk • 50
- Reputation:
- 50
- Status:
- New User
- Location:
- Last seen:
- 1 year, 7 months ago
- Joined:
- 3 years, 5 months ago
- Email:
- l***************@dzne.de
Posts by lech.kaczmarczyk
<prev
• 31 results •
page 1 of 4 •
next >
0
votes
1
answer
1.6k
views
1
answers
... Sorry, maybe I was not clear (or it is me, who simply don't get it):
My barcode+UMI will be located just upstream of the following primer:
**Multiplexing Read 2 Sequencing Primer
5' GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT**
In such a case,. I get the barcode+UMI sequence in the first 8 cycles. Isn't t ...
written 21 months ago by
lech.kaczmarczyk • 50
0
votes
1
answer
1.6k
views
1
answers
... My plan is to sequence only UMI and index using read2 (Reverse), so 8-9 cycles. Is there a problem with that? If this is for some reason (cost) inefficient approach, please let me know. ...
written 21 months ago by
lech.kaczmarczyk • 50
0
votes
0
answers
506
views
0
answers
... Hi Caleb,
I'd like to embark on using SLAM-seq. I was wondering if you made any progress with the half-life calculations in R?
Cheers,
Lech ...
written 21 months ago by
lech.kaczmarczyk • 50
0
votes
1
answer
1.6k
views
1
answers
... Barcodes embedded in the gene specific RT primers containing partial illumina adapters, below is the example (UMI and barcodes in bold). I don't have the reads yet as I'd like to have the strategy thought-through before starting. The experiment is aimed at assessing T->C conversions (SLAMseq) wit ...
written 21 months ago by
lech.kaczmarczyk • 50
0
votes
1
answer
1.6k
views
1
answers
... Thanks a lot, this is very informative. As this is not scRNAseq, and the barcodes represent individual samples, separate BAM per barcode would be ideal. I was also thinking about using FastX barcode splitter, after combining the pairs into one read after trimming, etc. Will try your solution!
...
written 21 months ago by
lech.kaczmarczyk • 50
1
vote
1
answer
1.6k
views
1
answer
... Hi All,
I'd like to demultiplex and deduplicate reads using in-line barcodes from read2 and UMIs from the read1 and read2. The format is like this (read2 is a short read, containing only barcode and UMI).
1:
UMI-primer-READ
2:
barcode-UMI
UMI-tools seems to be suitable, but I failed to find how t ...
written 21 months ago by
lech.kaczmarczyk • 50
• updated
21 months ago by
i.sudbery ♦ 11k
0
votes
0
answers
896
views
0
answers
... Thanks for that. Yes, I read that, but found it somehow not exhausting the topic. Sorry for my lack of understanding. ...
written 3.3 years ago by
lech.kaczmarczyk • 50
0
votes
1
answer
882
views
1
answer
... I would like to import a custom made pathway into Pathvisio. It only accepts GPML format. Is there any R package containing a relevant export function that I could use?
Cheers,
Lech ...
written 3.3 years ago by
lech.kaczmarczyk • 50
• updated
3.3 years ago by
Jean-Karim Heriche ♦ 24k
0
votes
0
answers
896
views
0
answers
... Hi All,
I am using QSEA to analyze MeDIP data. I am stuck on the step where enrichment parameters need to be defined (FUN `addEnrichmentParameters`). To get the rough idea about the data, I input the defaults. But now I would like to make sure they are the right choice. To quote the help of the FUN: ...
written 3.3 years ago by
lech.kaczmarczyk • 50
0
votes
1
answer
885
views
1
answers
... Thanks a bunch, good to know. ...
written 3.4 years ago by
lech.kaczmarczyk • 50
Latest awards to lech.kaczmarczyk
Popular Question
2.6 years ago,
created a question with more than 1,000 views.
For ENSEMBL IDs 2 Entrez Gene IDs - what to do if no match?
Popular Question
2.6 years ago,
created a question with more than 1,000 views.
For cell type-specific miRNA analysis and miRNA-mRNA expression correlation
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1895 users visited in the last hour