4
votes
10
replies
57
views
0
votes
5
replies
253
views
1
vote
1
reply
38
views
0
votes
2
replies
64
views
0
votes
1
reply
164
views
updated 3 hours ago by
lieven.sterck
15k
•
written 2 days ago by
Jl
•
0
1
vote
3
replies
92
views
0
votes
1
reply
65
views
updated 5 hours ago by
lieven.sterck
15k
•
written 6 hours ago by
Naila
•
0
835
votes
169
replies
172k
views
110 follow
updated 6 months ago by
Biostar
3.4k
•
written 8.3 years ago by
Istvan Albert
102k
1
vote
4
replies
100
views
4 hours ago by
SomeOne
▴
170
1
vote
7
replies
167
views
updated 6 hours ago by
yura.grabovska
▴
750
•
written 8 hours ago by
zhang616123
•
0
0
votes
2
replies
85
views
0
votes
0
replies
46
views
0
votes
0
replies
48
views
9 hours ago by
soledad.esteban
•
0
0
votes
4
replies
128
views
1
vote
14
replies
383
views
updated 11 hours ago by
colindaven
7.3k
•
written 1 day ago by
ZuelTech
•
0
1
vote
4
replies
812
views
updated 17 hours ago by
swbarnes2
14k
•
written 2 days ago by
Wu-Sheng Zhang
•
0
1
vote
4
replies
187
views
1
vote
6
replies
133
views
0
votes
1
reply
114
views
updated 20 hours ago by
chrchang523
11k
•
written 1 day ago by
Smilesky
•
0
0
votes
0
replies
59
views
0
votes
0
replies
73
views
1 day ago by
Physalia-courses
★
2.6k
0
votes
2
replies
130
views
0
votes
0
replies
78
views
1
vote
0
replies
166
views
0
votes
2
replies
252
views
0
votes
0
replies
167
views
updated 3 days ago by
Pierre Lindenbaum
165k
•
written 3 days ago by
swarnadurga66666m
•
0
0
votes
1
reply
195
views
updated 3 days ago by
GenoMax
150k
•
written 3 days ago by
Yongjie Zhang
▴
110
0
votes
1
reply
202
views
updated 3 days ago by
Mensur Dlakic
★
29k
•
written 3 days ago by
Yongjie Zhang
▴
110
2
votes
3
replies
2.3k
views
updated 3 days ago by
Dan A
•
0
•
written 3.7 years ago by
Agenor Neto
▴
10
1
vote
1
reply
227
views
0
votes
0
replies
159
views
0
votes
2
replies
293
views
updated 4 days ago by
Istvan Albert
102k
•
written 4 days ago by
louis-gil
•
0
2
votes
1
reply
418
views
0
votes
1
reply
491
views
3
votes
3
replies
379
views
0
votes
3
replies
1.6k
views
updated 4 days ago by
Bastien Hervé
6.2k
•
written 22 months ago by
Sun
•
0
0
votes
1
reply
241
views
0
votes
2
replies
809
views
3
votes
4
replies
3.3k
views
8
votes
3
replies
376
views
1
vote
1
reply
243
views
updated 5 days ago by
Ram
45k
•
written 5 days ago by
reddyraghuveer664
•
0
0
votes
0
replies
201
views
0
votes
1
reply
245
views
updated 5 days ago by
GenoMax
150k
•
written 5 days ago by
Placeholder@12654926
•
0
0
votes
1
reply
274
views
1
vote
1
reply
286
views
3
votes
2
replies
330
views
0
votes
1
reply
219
views
updated 1 hour ago by
Istvan Albert
102k
•
written 5 days ago by
laurasachica7
•
0
0
votes
4
replies
3.2k
views
updated 5 days ago by
Ram
45k
•
written 8.3 years ago by
roz_safavi
•
0
3
votes
6
replies
489
views
1
vote
0
replies
321
views
updated 6 days ago by
GenoMax
150k
•
written 6 days ago by
ilaria.palmisano
▴
10
Recent Votes
Recent Locations •
All
United States, 2 minutes ago
United States, 3 minutes ago
United States, 3 minutes ago
United States, 3 minutes ago
United States, 3 minutes ago
University Park, USA, 6 minutes ago
Memphis, TN, 6 minutes ago
Recent Awards •
All
Scholar to
Jiyao Wang
▴
380
Popular Question to
connorjfausto
▴
30
Popular Question to
timothy.kirkwood
▴
140
Scholar to
lieven.sterck
15k
Popular Question to
marco.barr
▴
170
Popular Question to
zizigolu
★
4.3k
Popular Question to
Physalia-courses
★
2.6k
Recent Replies
Comment: Batch correction RNA-seq analysis
by
ka132
•
0
Unfortunately, I just found out the libraries were prepped separately as well. Thanks for the advice!
Comment: Batch correction RNA-seq analysis
by
ka132
•
0
Well, dangit - I just heard back and the same sequencer was used but library prep was done separately. Bummer. Thanks for the assistance.
Comment: Batch correction RNA-seq analysis
by
jared.andrews07
★
18k
Batch correction as you mention shouldn't even run, I expect ComBat-seq will yell at you about confounded covariates if you try.
But as me…
Comment: Batch correction RNA-seq analysis
by
ka132
•
0
The actual experiment and collection of samples were done at same time. Library prep was definitely done by same person using same protocol…
Comment: Batch correction RNA-seq analysis
by
GenoMax
150k
There should be no appreciable batch effect because of sequencing, as long as following is true. The same sequencer (or at least type i.e. …
Comment: Batch correction RNA-seq analysis
by
ka132
•
0
yeah.... this is what I was afraid of. I wish this was a lesson that I needed to learn, but again I had no input on the processing up to th…
Comment: Batch correction RNA-seq analysis
by
ka132
•
0
Just sequencing, no common control unfortunately.
Comment: Batch correction RNA-seq analysis
by
GenoMax
150k
> samples were **run**
It would help if you clarify "run" part further. What exact part of the experiment was done in two batches. Full …
Comment: Wolfram tech for bio data analysis
by
GenoMax
150k
> Part of the motivation for this is that many universities have a full site-wide license for our software
Is there a publicly available l…
Answer: Batch correction RNA-seq analysis
by
jared.andrews07
★
18k
If you have no overlap between batches, there are unfortunately no real options. The experiment is confounded. Consider this an expensive a…
Comment: Filter snRNA-seq .fastq files based on barcodes
by
GenoMax
150k
`filterbyname.sh` only works based on information that is found in the **fastq header**. As you can see the barcodes you have are not in th…
Comment: Filter snRNA-seq .fastq files based on barcodes
by
GenoMax
150k
> How would I use the filtered bam files to get the fastq?
If you have the BAM files you can simply use `samtools fastq your.bam` with app…
Comment: VCFtools + easySFS snp # discordance
by
Istvan Albert
102k
this would not be easy to answer without seeing your VCF file - maybe you could share that VCF and people can take a look at it.
Comment: Filter snRNA-seq .fastq files based on barcodes
by
connorjfausto
▴
30
Yes these barcodes came from a Seurat Object aligned from `cellranger count`, I'll change the `.csv` file with your corrections and try. I …
Comment: Filter snRNA-seq .fastq files based on barcodes
by
connorjfausto
▴
30
Thanks for the response! Here's an example of an out when i input `zcat fq_r1.fastq.gz | head -n 10`
```
@A00738:690:HCNMKDSX7:3:1101:2102…
Traffic: 1832 users visited in the last hour
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
version 2.3.6
version 2.3.6