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868 results • Page
4 of 18
Sort: Votes
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Views
Votes
Replies
7
votes
5
replies
310
views
bcftools error: : error while loading shared libraries: libcrypto.so.1.0.0:
bcftools
4 days ago by
jiyoung
▴ 20
7
votes
13
replies
3.5k
views
6 follow
Is trimming necessary for RNAseq?
RNA-Seq
trimming
fastqc
updated 26 days ago by
ATpoint
78k • written 3.0 years ago by
Pac314
▴ 10
6
votes
3
replies
3.8k
views
How To Visualize Spliced Alignments Of Next Gen Sequencing Data?
splicing
next-gen-sequencing
visualization
updated 15 days ago by
Ram
41k • written 13.6 years ago by
Darked89
4.5k
6
votes
6
replies
414
views
6 follow
How to align a genome fasta file from NCBI to a reference genome?
genome
genetics
alignment
updated 6 days ago by
Antonio R. Franco
★ 5.1k • written 7 days ago by
ritafonsa
• 0
6
votes
5
replies
3.0k
views
Multi threading bowtie index
bowtie
indexing
updated 4 days ago by
colindaven
5.7k • written 8.2 years ago by
ChillarAnand
▴ 70
6
votes
1
reply
267
views
How to retrieve sample informations from given ID from Sequence Read Archives?
eutils
SRA
updated 12 days ago by
Ram
41k • written 10 weeks ago by
DareDevil
★ 3.3k
6
votes
2
replies
2.7k
views
Adjacency Files For Abyss-Explorer
assembly
visualization
updated 21 days ago by
Ram
41k • written 13.7 years ago by
2184687-1231-83-
★ 5.1k
6
votes
7
replies
1.9k
views
2D structure of a custom protein (not in any databases) from a PDB file.
PDB
protein-structure
Pymol
updated 29 days ago by
Wayne
★ 1.8k • written 10 months ago by
Hansen_869
▴ 60
6
votes
12
replies
907
views
Building reference dbSNP file for citrus sinensis using 80 WGS samples
NGS
WGS
Variant-calling
non-model
Bootstrapping
updated 19 days ago by
Brian Bushnell
19k • written 6 weeks ago by
analyst
▴ 10
6
votes
6
replies
395
views
6 follow
STAR alignment speed
STAR
alignment
RNA
updated 6 days ago by
ATpoint
78k • written 8 days ago by
Gilles
• 0
6
votes
3
replies
4.2k
views
Ngs: How Many Reads Should Be Expected To Map To The Reference Sequence
next-gen-sequencing
short-read-aligner
updated 15 days ago by
Ram
41k • written 13.6 years ago by
Allpowerde
★ 1.3k
6
votes
4
replies
1.3k
views
Effect of Bootstrapping/Gibbs Sampling in Salmon Counts
Gibbs
Bootstrapping
RNAseq
Salmon
Sampling
updated 16 days ago by
Gordon Smyth
★ 6.5k • written 18 months ago by
saipra003
▴ 10
6
votes
7
replies
5.1k
views
Failed To Connect To The Ensembl Mysql Database
mysql
ensembl
updated 21 days ago by
Ram
41k • written 13.7 years ago by
Fred Fleche
4.3k
6
votes
7
replies
8.0k
views
6 follow
Abyss Output File Formats
assembly
abyss
updated 15 days ago by
Ram
41k • written 13.6 years ago by
Rob Syme
▴ 540
6
votes
2
replies
351
views
How to obtain data on the specific location of the segumental duplication.
UCSC
duplication
segemental
8 days ago by
ayasu
• 0
6
votes
3
replies
3.3k
views
Rna Data Sources???...Please Help
rna
secondary
updated 15 days ago by
Ram
41k • written 13.6 years ago by
Suhail
▴ 10
6
votes
3
replies
254
views
BBDuk error: with these 4 lines....
BBDUK
trimming
java
1 day ago by
blackadder
▴ 30
5
votes
6
replies
2.8k
views
MACS3 installation
python3
cykhash
MACS3
cython
updated 27 days ago by
rpolicastro
12k • written 23 months ago by
c.eskiw
▴ 10
5
votes
2
replies
235
views
RNA Contamination Tool for Developing Cell Samples
contamination
scRNA
quality
RNA
SoupX
4 days ago by
Rafael Soler
★ 1.2k
5
votes
5
replies
328
views
SP500 useable read lengths
Illumina
NovaSeq
NGS
updated 25 days ago by
GenoMax
136k • written 25 days ago by
joe
▴ 390
5
votes
3
replies
321
views
Strand bias in supplementary alignments from Nanopore
minimap2
nanopore
strand
updated 21 days ago by
cmdcolin
★ 3.4k • written 21 days ago by
dariober
14k
5
votes
7
replies
555
views
Paired-end RNA seq (NextSeq2000): 1-3% if R2 reads are only contain G bases
RNA-seq
19 days ago by
Jurgen
• 0
5
votes
4
replies
316
views
Filter out ALT contigs from CRAM
CRAM
updated 7 days ago by
Istvan Albert
99k • written 8 days ago by
German.M.Demidov
★ 2.9k
5
votes
8
replies
629
views
UCSC custom track upload direct data POST / without url
api
ucsc
updated 15 days ago by
Maximilian Haeussler
★ 1.6k • written 21 days ago by
San
▴ 10
5
votes
8
replies
602
views
duplicates issues when trying to convert long to wide in R
R
18 days ago by
happyday1661
• 0
5
votes
5
replies
379
views
6 follow
Finding exons that are always included
alternative-splicing
exon
updated 20 days ago by
Jeremy Leipzig
22k • written 20 days ago by
smurph50
▴ 50
5
votes
13
replies
858
views
Is my data too noisy for DESeq? Should I model noise as unwanted variation?
rna-seq
deseq
updated 12 days ago by
LauferVA
3.8k • written 21 days ago by
Ben
▴ 10
5
votes
5
replies
2.2k
views
Quickly retrieve reference genome sequence within python
sequence
python
updated 28 days ago by
Feng Tian
▴ 20 • written 5.2 years ago by
gewa
▴ 20
5
votes
11
replies
617
views
question regarding the labeling of points on graphs generated by ggplot in R
R
ggplot
updated 25 days ago by
rpolicastro
12k • written 25 days ago by
Francois Piumi
▴ 40
5
votes
5
replies
6.1k
views
6 follow
Mitochondrial genes in single cell nuclear RNAseq data
RNA-Seq
gene
mitochondria
updated 5 days ago by
Prakki Rama
★ 2.7k • written 4.9 years ago by
dalhoomist
▴ 40
5
votes
8
replies
3.6k
views
Sufficient Specs for a laptop to work in bioinformatics
hardware
NGS
updated 14 days ago by
ashaneev07
▴ 20 • written 20 months ago by
ashwing.kofficial
▴ 10
5
votes
4
replies
447
views
FASTQ to BAM to CRAM to FASTQ
Samtools
29 days ago by
ManuelDB
▴ 70
5
votes
10
replies
598
views
Different number of reads when converting data from FASTQ to BAM and CRAM to FASTQ
picard
28 days ago by
ManuelDB
▴ 70
5
votes
2
replies
1.8k
views
Biopython error: "ModuleNotFoundError: No module named 'Bio.SubsMat'"
biopython
updated 14 days ago by
IkramInf
▴ 20 • written 7 months ago by
Alexander
▴ 200
5
votes
6
replies
3.8k
views
Accessing Cyanobase With The Biomart / Getbm Method
biomart
r
updated 21 days ago by
Ram
41k • written 13.7 years ago by
John
▴ 790
5
votes
3
replies
199
views
SPAdes error: finished abnormally, OS return value: 21
SPAdes
updated 10 hours ago by
Brian Bushnell
19k • written 1 day ago by
jiyoung
▴ 20
5
votes
4
replies
348
views
Conda environment not named
snakemake
conda
updated 21 days ago by
Ram
41k • written 21 days ago by
Begonia_pavonina
▴ 120
5
votes
1
reply
237
views
How does tabix work?
annotation
tabix
ngs
vcf
updated 26 days ago by
Pierre Lindenbaum
158k • written 26 days ago by
captainlabman
▴ 10
5
votes
0
replies
4.2k
views
Tutorial:
Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
21 days ago by
GenoMax
136k
5
votes
3
replies
230
views
How to overlap patient VCF with ClinVar database annotation using bedtools?
bedtools
bash
ClinVar
overlap
VCF
updated 7 days ago by
Ram
41k • written 7 days ago by
Muffin Man
▴ 10
4
votes
4
replies
459
views
Calculating height prediction from PGS
polygenic-score
14 days ago by
fitwae
• 0
4
votes
2
replies
388
views
Does DESeq2 correct for library size when importing the counts with DESeqDataSetFromMatrix?
rna-seq
deseq2
updated 10 days ago by
i.sudbery
18k • written 12 days ago by
bioinfo
▴ 140
4
votes
6
replies
372
views
Unexpected separation of RNA-seq samples on PCA plot
depletion
PCA
rRNA
plot
RNA-seq
8 days ago by
Tihana
▴ 10
4
votes
4
replies
344
views
bwa-mem2 error: skip or orientatioon FF
bwa-mem2
15 days ago by
jiyoung
▴ 20
4
votes
4
replies
372
views
Best way to use k-mers as a predictor in my neural network
convolutional-neural-network
kmer
updated 27 days ago by
Brian Bushnell
19k • written 28 days ago by
Jimmy
▴ 10
4
votes
8
replies
1.6k
views
Same sequencing sample in multiple lanes. How to analyse it?
sequencing
bowtie2
alignment
samtools
ngs
updated 15 days ago by
Istvan Albert
99k • written 21 months ago by
Federico
• 0
4
votes
4
replies
558
views
Combining GO and KEGG enrichments
Cytoscape
KEGG
network
RNASeq
GO
11 days ago by
David R
▴ 20
4
votes
3
replies
7.1k
views
Are XA: tagged reads == SA: tagged BWAMEM aligned reads?
bam
bwa-mem
samtools
updated 25 days ago by
xiaoleiusc
▴ 120 • written 8.0 years ago by
QVINTVS_FABIVS_MAXIMVS
★ 2.5k
4
votes
9
replies
29k
views
8 follow
How To Get Chromosome Position Given Rs Number?
snp
chromosome
position
updated 15 days ago by
GenoMax
136k • written 10.0 years ago by
chrismas05
• 0
4
votes
6
replies
520
views
BLAST hits on viruses relate to different host than used
Phage
BLAST
Metagenomics
3 days ago by
DonPhager
• 0
868 results • Page
4 of 18
Recent Votes
Answer: How should I run ssgsea analysis ?
Comment: Parsing XML file from dbGaP
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
Comment: SPAdes error: finished abnormally, OS return value: 21
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
Comment: unicycler error : [Errno 13] Permission denied:
Comment: unicycler error : [Errno 13] Permission denied:
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Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
by
CTLong
▴ 10
That makes sense. Thanks for the reminder.
Comment: bwa mem hangs after a few thousand reads
by
GenoMax
136k
Then you probably are best served by talking with your local sys admins to see where the issue may be.
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
by
GenoMax
136k
> even if tpe and tbo are trailing after adapter and quality trimming Priority/order of operations in coded in the program. Brian will be …
Comment: bwa mem hangs after a few thousand reads
by
cee28
• 0
Actually, I originally did both of those things that you suggested. My original command at the top of the post was submitted to our cluster…
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
by
CTLong
▴ 10
The number of bases is still different even if `tpe` and `tbo` are trailing after adapter and quality trimming. So far for the RNA-seq proj…
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
by
GenoMax
136k
No there should not be much impact unless one of the reads has become substantially short compared to its mate. Strictly speaking you don't…
Comment: bwa mem hangs after a few thousand reads
by
GenoMax
136k
> I am running this on a HPC cluster. This is a guess but if you are actually running this on a cluster then it is possible that you need …
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
by
CTLong
▴ 10
Thanks GenoMax for the reply. That being said, does this difference in total bases between read1 and read2 have an effect in subsequent rea…
Comment: CHIPSEQ : Cut AND Run , DiffBind Parameters
by
DINESHR
• 0
Here are my PCA results plotted through Diffbind and Correlation heat map by deeptools shows some clustering in the samples @atpoint ![e…
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
by
dsull
★ 5.0k
Yeah, sometimes it looks "prettier" to plot p-value rather than adjusted p-value; although either one is technically ok to plot (even multi…
Comment: How to get unaligned reads and aligned reads into separate files from SAM/BAM?
by
rpolicastro
12k
I suppose if you really wanted to do it in one pass pysam would be an option. Courtesy of ChatGPT with a few modifications, and tested to s…
Comment: frequency plot for peaks
by
Ankit
▴ 400
what is your txdb? can you explain your experiment in detail?
Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when
by
cmdcolin
★ 3.4k
paste the file in csv format and a R wizard might come along and help :)
Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when
by
rpolicastro
12k
Your intuition was correct. You want to make two separate data frames and join them on sample name. This code is untested but will probably…
Comment: Generate Read counts from bam file
by
ATpoint
78k
It has nothing to do with low complexity. You always map to the entire genome since the reads can come from the entire genome. If you take …
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