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1,000 results • Page
1 of 20
Sort: Views
Rank
Views
Votes
Replies
9
votes
13
replies
15k
views
Sort bam file by coordinates using samtools
next-gen-sequencing
gene
rna-seq
updated 9 months ago by
Ram
43k • written 5.5 years ago by
Shahzad
▴ 30
16
votes
7
replies
12k
views
8 follow
MAF vs VAF
sequencing
updated 3 days ago by
Ömer An
▴ 260 • written 6.0 years ago by
lauren.wahyudi
▴ 50
3
votes
16
replies
11k
views
combining z-scores into a single z-score value
excel
R
statistics
updated 10 months ago by
Ram
43k • written 5.0 years ago by
Star
▴ 60
0
votes
8
replies
9.8k
views
how to find a read by name in a bam file
next-gen-sequencing
updated 9 months ago by
Ram
43k • written 6.7 years ago by
himanimalhotra89
• 0
7
votes
8
replies
8.9k
views
Determining read count
trimmomatic
rna-seq
trinity
updated 7 months ago by
Ram
43k • written 7.9 years ago by
nikelle.petrillo
▴ 110
4
votes
12
replies
7.6k
views
6 follow
BWA error: no ID within the read group line
bwa
readgroups
RG
parallel
updated 7 weeks ago by
mgdrnl
▴ 10 • written 3.3 years ago by
whb
▴ 60
4
votes
45
replies
7.5k
views
SAM file wrong? help with validatesamfile
EXOME
updated 11 months ago by
Ram
43k • written 7.8 years ago by
cristina_sabiers
▴ 110
2
votes
9
replies
7.4k
views
6 follow
Read MAP and PED files in PLINK
GWAS
PLINK
updated 3 months ago by
GenoMax
140k • written 5.9 years ago by
ft821525
• 0
0
votes
7
replies
7.1k
views
Problem in in alignment by muscle
sequence
muscle
alignment
updated 9 months ago by
Ram
43k • written 6.6 years ago by
misbahabas
▴ 70
6
votes
4
replies
6.3k
views
What is gnomAD allele frequency
AF
gnomAD
updated 10 weeks ago by
Lhl
▴ 760 • written 3.0 years ago by
Eric Wang
▴ 50
3
votes
7
replies
6.3k
views
Human reference files in HG38 GATK resource bundle
VCF
updated 10 months ago by
DareDevil
★ 4.3k • written 6.2 years ago by
win
▴ 970
3
votes
7
replies
6.2k
views
running trimmomatic inside Trinity
Assembly
Trinity
RNA-seq
trimmomatic
updated 9 months ago by
Ram
43k • written 8.0 years ago by
lay_0
▴ 50
0
votes
3
replies
6.2k
views
fastq-dump: command not found, what is wrong?
assembly
sratoolkit
genomics
updated 9 months ago by
Ram
43k • written 2.6 years ago by
BioinfoNoob6
• 0
2
votes
14
replies
5.8k
views
Using sam-dump in SRA toolkit to download chr20.bam from NA12878
sratoolkit
sam-dump
updated 9 months ago by
Ram
43k • written 7.0 years ago by
Covux
▴ 10
0
votes
4
replies
5.8k
views
using IGV to visualize RNA seq alignment to transcriptome
rna-seq
igv
alignment
updated 7 months ago by
Ram
43k • written 7.8 years ago by
nikelle.petrillo
▴ 110
1
vote
5
replies
5.8k
views
Generate VCF File from Bam file and fasta by GATK
vcf
SNP
genome
next-gen
updated 9 months ago by
Ram
43k • written 6.7 years ago by
misbahabas
▴ 70
0
votes
4
replies
5.7k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 9 months ago by
Franco
• 0 • written 6.4 years ago by
ac.research
▴ 30
0
votes
7
replies
5.7k
views
save command output to a file in pymol
pymol
python
updated 11 months ago by
Ram
43k • written 7.2 years ago by
ac.research
▴ 30
3
votes
14
replies
5.7k
views
remote command line BLAST job ends in CPU error and gives MBEDTLS version mismatch
blastn
mbedtls
blast
linux
blast+
updated 9 weeks ago by
K.Gee
▴ 40 • written 3.0 years ago by
janneken0210
• 0
1
vote
10
replies
5.7k
views
which field has more scope Bioinformatics or Biomedical engineering at MS level???
biomedical
updated 11 months ago by
Ram
43k • written 7.6 years ago by
purpledora100
• 0
1
vote
3
replies
5.6k
views
Use samtools to access bam file in aws s3 storage
samtools
updated 11 months ago by
Ram
43k • written 7.5 years ago by
xing
▴ 10
0
votes
3
replies
5.5k
views
Bedgraphtobigwig Conversion Difficulties
bigwig
updated 8 months ago by
Ram
43k • written 11.1 years ago by
stu.andrews
• 0
1
vote
2
replies
5.5k
views
sortmerna command not working
NGS
RNA-Seq
sortmerna
updated 11 months ago by
Ram
43k • written 7.9 years ago by
Shahzad
▴ 30
0
votes
2
replies
5.5k
views
GDC Data Portal
collaboration
updated 11 months ago by
Ram
43k • written 7.5 years ago by
ranlab
• 0
1
vote
4
replies
5.4k
views
Conditionally coloring the fold change values to plot a heatmap using pheatmap
R
heatmap
updated 10 months ago by
Ram
43k • written 6.1 years ago by
chetana
▴ 60
3
votes
4
replies
5.4k
views
How to visualize sequence quality control distribution
sequence
Fastq
R
updated 12 months ago by
Ram
43k • written 8.4 years ago by
faizlotfy
▴ 30
0
votes
9
replies
5.3k
views
Calculating FPKM and TPM by hand from htseq-count output?
RNA-Seq
rna-seq
htseq
FPKM
TPM
updated 7 months ago by
ATpoint
81k • written 5.0 years ago by
Joel Wallenius
▴ 210
0
votes
1
reply
5.3k
views
Hapmap to vcf
vcf
hapmap
updated 8 months ago by
Ram
43k • written 5.5 years ago by
shinken123
▴ 150
0
votes
4
replies
5.2k
views
Sequence alignment length
multiple-sequence-alignment
updated 10 months ago by
Ram
43k • written 7.2 years ago by
biobudhan
▴ 20
3
votes
4
replies
5.1k
views
What does this Warning in HTSeq-count means? (Warning: Mate pairing was ambiguous)
RNA-Seq
updated 8 months ago by
tirza.doniger
▴ 10 • written 8.6 years ago by
tiago211287
★ 1.4k
2
votes
11
replies
5.1k
views
How long it takes to run repeat masker on a full genome
Assembly
updated 10 weeks ago by
e.r.zakiev
▴ 170 • written 7.7 years ago by
CAnna
▴ 20
7
votes
7
replies
4.9k
views
RNA-Seq time series analysis using a DESeq2 spline approach yields far too many significant genes
splines
DESeq2
time-series
RNA-Seq
updated 10 months ago by
Ram
43k • written 5.2 years ago by
stu111538
▴ 80
10
votes
14
replies
4.8k
views
ATAC-seq data and deepTools: Small detail with impact on output
bigwig
read-length
deeptools
ATAC-seq
updated 9 months ago by
Ram
43k • written 4.1 years ago by
gable_works
▴ 50
1
vote
4
replies
4.7k
views
TCGA data(RPKM) differential gene expression
rna-seq
R
TCGA
RPKM
IPA
8 months ago by
realnewbie
▴ 30
3
votes
2
replies
4.7k
views
How to plot a circular clustered heatmap with dendrogram
circular heatmap
updated 7 months ago by
logbio
▴ 30 • written 4.4 years ago by
The
▴ 180
2
votes
7
replies
4.6k
views
SRA toolkit internet settings
sratoolkit
fastq-dump
sequencing
RNA-Seq
updated 9 months ago by
Ram
43k • written 7.6 years ago by
BCArg
▴ 90
0
votes
8
replies
4.4k
views
Downloading single cell data from NCBI
ncbi
rna-seq
fastq-dump
single-cell
updated 7 months ago by
Ram
43k • written 5.3 years ago by
V
▴ 380
0
votes
7
replies
4.4k
views
align_and_estimate_abundance.pl (rsem-parse-alignments: /lib64/libz.so.1: version `ZLIB_1.2.3.3' not found (required by rsem-parse-alignments))
RNA-Seq
alignment
software-error
next-gen
sequence
updated 3 months ago by
Ram
43k • written 5.9 years ago by
nasreenbano91
• 0
1
vote
0
replies
4.4k
views
how to convert .geno/.snp/.ind to .bed/.bim/.fam (ped plink format) in Windows
plink
genomes
ancestrymap
updated 8 months ago by
Ram
43k • written 7.8 years ago by
Ghoul
▴ 10
3
votes
4
replies
4.3k
views
Atypical volcano plot RNA-seq
volcano-plot
RNA-seq
deseq2
updated 7 months ago by
Ram
43k • written 5.4 years ago by
Teresa
▴ 20
2
votes
10
replies
4.2k
views
Error encountered while running stattest from ballgown package
bioconductor
RNA-Seq
ballgown
stattest
updated 11 months ago by
Ram
43k • written 6.9 years ago by
lakhujanivijay
5.8k
7
votes
13
replies
4.2k
views
6 follow
Is trimming necessary for RNAseq?
RNA-Seq
trimming
fastqc
updated 4 months ago by
ATpoint
81k • written 3.4 years ago by
Pac314
▴ 10
7
votes
8
replies
4.1k
views
DEseq2 design matrix with 3 factors
RNA-seq
deseq2
updated 9 months ago by
Ram
43k • written 3.8 years ago by
kand3e
▴ 60
1
vote
9
replies
4.1k
views
Unable to install bioconda and bowtie
bioconda
conda
updated 3 months ago by
rpolicastro
13k • written 18 months ago by
n.anuragsharma
▴ 30
0
votes
4
replies
4.1k
views
What is Dunn's multiple comparison test?
statistics
updated 10 months ago by
Ram
43k • written 6.6 years ago by
Koreanraichu
• 0
3
votes
4
replies
4.0k
views
What are the Pros and Cons of working in Bioinformatics???
career
bio
updated 10 months ago by
Ram
43k • written 6.1 years ago by
scottschu97
▴ 20
2
votes
4
replies
4.0k
views
Transcriptomic Coordinate Bam To Genomic Coordinate Bam
bam
genomics
updated 8 months ago by
Ram
43k • written 11.2 years ago by
Ge
▴ 80
1
vote
7
replies
4.0k
views
Adjust width of annotations in pheatmap
R
heatmap
updated 5 months ago by
Kevin Blighe
87k • written 5.4 years ago by
divya.nandakumar
▴ 30
1
vote
5
replies
3.9k
views
Time-series or pairwise comparison EdgeR - what's more suited?
DGE-analysis
Time-series
pairwise
updated 10 months ago by
Ram
43k • written 7.6 years ago by
Biogeek
▴ 470
5
votes
19
replies
3.9k
views
8 follow
Hisat2 aligner problem
RNA-Seq
ChIP-Seq
alignment
Assembly
software error
updated 3 months ago by
ATpoint
81k • written 4.8 years ago by
ta_awwad
▴ 340
1,000 results • Page
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Comment: Interproscan taking so much time
Answer: Interproscan taking so much time
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Answer: Issue with making local BLAST database
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Comment: FindAllMarkers not working (Error (data layers are not joined. Please run JoinL
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I tried that too. It did not work.
Comment: (sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
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140k
Try SRA-explorer with search terms you want. Guide here: https://www.biostars.org/p/366721/ Check these portals: https://singlecell.broad…
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Thank you @genomax, if I have well understood the `retmax` parameter and 10000 entries limitation are linked to the R package, and not to t…
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thank you , this is my code : import sys import os import subprocess class FastpFiltering: def __init__(self, input_folder, fastp_ou…
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You can also use `reformat.sh` from [**BBMap suite**][1]. Look at sampling options. [1]: https://sourceforge.net/projects/bbmap/
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> I was using it but the output file was too big pipe the output
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Share code and an example please.
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I was using it but the output file was too big, so that I thought the vcf file was more efficient. But now I know that I can stop working o…
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Thank you for your reply. I have just executed the computation with parallelization as you mentioned, and I will observe the differences. H…
Comment: struggle to get fasta files from ucsc goldenPath
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Lila M
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Of course ... But as 'expected' the range `range=chr8:127794533-128101253` in the output sequence file belongs to: LF385466, LF385467, MA62…
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by
GenoMax
140k
Can you select the output format as sequence instead of BED?
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
Could you please elaborate how to retrieve the sequences directly from the table browser? Thanks!
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140k
If coordinates in your BED file refer to chromosomal locations then you need to use the whole genome file and get those sections by the met…
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maybe it would work better to ask the OP to post their question as a new one and delete this answer after, if you delete the post they ca…
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GenoMax
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By default only 20 entries are returned if you don't set the `retmax` parameter. You will not want to do this via R since you will be limit…
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