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1,389 results • Page
1 of 28
Sort: Rank
Rank
Views
Votes
Replies
Filtering for tag:
BAM
•
reset
2
votes
3
replies
168
views
Remove reads from bam file that partially covers a region
indel
filter
bam
14 hours ago by
arbarharw
• 0
42
votes
7
replies
31k
views
8 follow
Any Good Bam And Sam Viewer?
viewer
sam
bam
updated 5 days ago by
dariober
12k • written 9.5 years ago by
Ken
▴ 150
0
votes
0
replies
52
views
How to calculate differential coverage between two groups?
differential
bed
bam
rnaseq
coverage
5 days ago by
O.rka
▴ 290
0
votes
7
replies
172
views
remove unmapped reads on a specific chromosome only
bam
remove
unmapped
updated 5 days ago by
i.sudbery
11k • written 6 days ago by
firatuyulur
▴ 310
0
votes
0
replies
42
views
Active regions determination in HaplotypeCaller
SNP
GATK
VCF
HaplotypeCaller
BAM
6 days ago by
Nawar
• 0
0
votes
1
reply
88
views
How to generate bam files containing the entire read alignments?
bam
RNAseq
reads
alignment
updated 6 days ago by
Carlo Yague
5.8k • written 6 days ago by
Arman
• 0
0
votes
3
replies
192
views
How to extract consensus sequence for a genomic region from a bam file
samtools
bam
6 days ago by
michael.flower.14
• 0
6
votes
5
replies
2.6k
views
tool for bam soft clipping reads within bed file regions
bam
clipping
bed
updated 7 days ago by
Pierre Lindenbaum
135k • written 5.1 years ago by
14134125465346445
★ 3.5k
0
votes
11
replies
303
views
Extracting reads from one barcode in a bam file
extract
bam
barcode
7 days ago by
msrinivasan
• 0
1
vote
4
replies
249
views
BAM file's reference sequence IDs doesnt match contigs ID's
files
metagenomics
alignment
bam
binning
7 days ago by
v.berriosfarias
▴ 10
0
votes
0
replies
80
views
How important is aligning BAM files to the appropriate design file?
gatk
sequencing
genomics
wes
bam
12 days ago by
jon.klonowski
▴ 70
2
votes
2
replies
192
views
Infering strand specificity of bam files using rseqc?
RSeQC
bam
featureCounts
updated 14 days ago by
Istvan Albert
87k • written 14 days ago by
dare_devil
★ 1.4k
5
votes
2
replies
217
views
Could I analyze just a few genes of a BAM file?
RNA-Seq
BAM
updated 14 days ago by
seidel
7.6k • written 14 days ago by
abdi.zhr26
• 0
2
votes
3
replies
213
views
BAM file download for just a few genes
RefSeq
BAM
position
RNA-Seq
UCSC
updated 16 days ago by
Jorge Amigo
12k • written 16 days ago by
abdi.zhr26
• 0
6
votes
6
replies
1.9k
views
6 follow
Issue With CRAM -> BAM -> FASTQ Conversion
samtools
fastq
cram
bam
view
updated 18 days ago by
bw.
▴ 160 • written 21 months ago by
denis.k
▴ 20
0
votes
12
replies
530
views
Write free text comment with @CO in BAM file
BAM
hstjdk
java
19 days ago by
mhasa006
▴ 50
2
votes
2
replies
121
views
Difference between read depth, allelic depth and bam readcounts
bam
vcf
sequencing
genotype
updated 26 days ago by
binodregmi30
▴ 10 • written 26 days ago by
lincaijin1994
• 0
2
votes
2
replies
119
views
Sequencing Information from BAM file
RNA-Seq
BAM
alignment
Library
26 days ago by
MarVi
▴ 20
0
votes
0
replies
85
views
Should i calculated Nm, UQ and MD tag of bam ?
alignment
bam
gatk
27 days ago by
quentin54520
• 0
0
votes
0
replies
119
views
Any tool to mask specific probe sequence in an alignment bam file
bam
masking
probe
28 days ago by
Ken
▴ 10
0
votes
0
replies
106
views
filtering issue when using bamCoverage
alignment
sequencing
bam
bamCoverage
deepTools
4 weeks ago by
Gimena
• 0
1
vote
15
replies
283
views
Picard ValidateSamFile Error: "ValidateSamFile Value was put into PairInfoMap more than once"
samtools
bam
sam
picard
alignment
12 days ago by
stephen.johnson.online
• 0
1
vote
4
replies
99
views
Malformed BAM while running GATK
GATK
BAM
Read group
Barcode
5 weeks ago by
shivangi.agarwal800
▴ 70
0
votes
3
replies
134
views
Bam files not accepted in dba.count
samtools
diffbind
dba.count
bam
5 weeks ago by
corinne_hutfilz
• 0
0
votes
1
reply
86
views
Effective subsampling of BAMs
BAM
sampling
updated 5 weeks ago by
ATpoint
47k • written 5 weeks ago by
esimonova.me
▴ 10
0
votes
0
replies
91
views
Horizontal sub-windows for IGV
IGV
bam
6 weeks ago by
German.M.Demidov
★ 2.0k
2
votes
1
reply
105
views
BAM FLAG mate unmappedand mate reverse strand
BAM
updated 6 weeks ago by
i.sudbery
11k • written 6 weeks ago by
esimonova.me
▴ 10
1
vote
1
reply
2.2k
views
Samtools Mpileup Doesn'T Show Deletion, When Deletion Between Paddings
samtools
mpileup
bam
ngs
updated 7 weeks ago by
aroob.lab
• 0 • written 8.0 years ago by
tsk
▴ 10
29
votes
11
replies
3.7k
views
7 follow
Tutorial:
Generating consensus sequence from bam file
bam
fasta
consensus
Tutorial
updated 7 weeks ago by
zjamal.msbi19rcms
• 0 • written 2.1 years ago by
finswimmer
14k
0
votes
6
replies
117
views
Estimate edit distance to a reference for a subset of bases in reads (bam files)
next-gen
bam
samtools
sequence
updated 7 weeks ago by
Pierre Lindenbaum
135k • written 7 weeks ago by
AQ7
▴ 30
0
votes
5
replies
173
views
Issue when merging FastQ
Fastq
Merging
mapping
SAM
BAM
updated 8 weeks ago by
Biostar
20 • written 12 weeks ago by
gayal25016
• 0
2
votes
3
replies
167
views
Convert processed bam file to fastq
alignment
sequence
bam
samtools
fastq
updated 8 weeks ago by
GenoMax
99k • written 8 weeks ago by
coltonrobbins73
• 0
0
votes
2
replies
120
views
extract split-read from bam/cram file
bam
cram
split-read
soft clip
8 weeks ago by
obaid_lama
• 0
5
votes
4
replies
156
views
Converting CRAM to BAM without reference fasta
samtools
BAM
CRAM
9 weeks ago by
Ld_60
▴ 40
1
vote
2
replies
168
views
featureCounts paired end mode
featureCounts
subread
bam
paired
RNA-Seq
updated 9 weeks ago by
Carlo Yague
5.8k • written 9 weeks ago by
henry-keen
▴ 20
22
votes
20
replies
2.9k
views
Tool:
elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMtools for processing SAM/BAM files
sam
bam
markduplicates
sort
bqsr
Tool
9 weeks ago by
Charlotte.Herzeel
▴ 150
1
vote
4
replies
426
views
pysam error when reading .bam file ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format?
pysam
bam
sam
updated 9 weeks ago by
Biostar
20 • written 9 weeks ago by
daewowo
• 0
0
votes
4
replies
158
views
Server to host bam files
RNA-Seq
alignment
bam
9 weeks ago by
vkkodali
★ 2.5k
0
votes
1
reply
141
views
Efficient way to download all .bam files in a project from ENA to remote server
bam
download
ENA
9 weeks ago by
4galaxy77
▴ 390
0
votes
0
replies
143
views
bamToFastq on Sequel subreads.bam
PacBio
bam
subreads
9 weeks ago by
christian.dreischer
• 0
76
votes
24
replies
68k
views
18 follow
How To Split A Bam File By Chromosome
bam
split
chromosome
updated 9 weeks ago by
opplatek
▴ 100 • written 8.9 years ago by
GPR
▴ 330
0
votes
1
reply
1.2k
views
interpolation y vector
sequencing
matlab
samtools
bam
updated 9 weeks ago by
Biostar
20 • written 6.2 years ago by
mosquitoes
• 0
10
votes
11
replies
15k
views
6 follow
How to determine reference genome that was used for alignment given BAM with obscure or no header
BAM
Reference
alignment
Reference Genome
updated 10 weeks ago by
c_u
▴ 290 • written 5.8 years ago by
Irene@Sequencing.com
▴ 260
5
votes
7
replies
188
views
bedtools intersect usage problem
bedtools
intersect
bam
updated 10 weeks ago by
i.sudbery
11k • written 10 weeks ago by
ja4123
• 0
0
votes
5
replies
150
views
Error-rate of a subset of the genome
WGS
error
bam
bed
10 weeks ago by
skanterakis
▴ 110
0
votes
1
reply
147
views
How to sort a FASTA file and (its) BAM file in the same order?
fasta
bam
samtools
10 weeks ago by
Dunois
▴ 620
1
vote
3
replies
1.0k
views
Might @PG headers affect downstream analyses, and how can I safely remove them from a BAM file?
bam
@PG
read groups
updated 11 weeks ago by
bjwiley23
▴ 20 • written 2.1 years ago by
olikidrod
• 0
1
vote
1
reply
383
views
Getting all the genomic coordinates where RNA-seq reads are split within a given genomic interval in a bam file
RNA-Seq
bam
splicing
cigar
reads
updated 12 weeks ago by
Pierre Lindenbaum
135k • written 12 weeks ago by
rubic
▴ 210
6
votes
5
replies
188
views
How to check size of genome?
bam
bp
updated 12 weeks ago by
Alex Reynolds
32k • written 12 weeks ago by
arianc
• 0
3
votes
3
replies
504
views
How to convert fastq to bam?
fastq
bam
updated 3 months ago by
ATpoint
47k • written 3 months ago by
arianc
• 0
1,389 results • Page
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Recent Votes
Comment: why my volcano plot looks strange?
C: how to choose hub genes in wgcna
C: Variant Calls: Freebayes vs GATK
C: Variant Calls: Freebayes vs GATK
A: FreeBayes vs GATK's HaplotypeCaller
Comment: why my volcano plot looks strange?
Answer: What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
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Comment: FreeBayes vs GATK's HaplotypeCaller
by
cicindel
▴ 70
I think file size, based on the following sentence.
Comment: How to perform multiple alignment using MAFFT?
by
Ram
32k
I don't see `GENE` being assigned values, so I'm guessing there is yet another loop wrapping the code above. Write the value of `GENE` to s…
Comment: What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
by
cicindel
▴ 70
Interesting, I did not think about it like that. Tablet has several colour schemes in the 2nd tab (I think) to visualize different features…
Answer: Trimmomatic-0.36 not finding adapter directory
by
Istvan Albert
87k
Download the adapters and use them by passing the actual path, existing paths to the adapter file. See the adapters here https://git…
Comment: What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
by
Istvan Albert
87k
in all fairness, Tablet did not exist when this thread was started. It is quite impressive that Tablet is still operational though, I gave …
Comment: Trimmomatic-0.36 not finding adapter directory
by
GenoMax
99k
Order of `fastq` file names is important for `trimmomatic`. Make sure that is correct.<br> Does `ls -lh /usr/local/bin/Trimmomatic-0.36/` …
Answer: What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
by
cicindel
▴ 70
No love for [Tablet][1]? I'm quite surprised to not see it mentioned here. Of course, IGV is the classic, and Tablet is a bit simpler than …
Comment: How to download raw sequence data from GEO/SRA
by
cicindel
▴ 70
I tried to use the SRA toolkit a few months ago, I succesfully installed it and used `prefetch` to get the data, as per their tutorial, but…
Comment: Concatenating fasta files based on prefix ?
by
cpad0112
15k
If each group has `._1_1.txt.fa` and the pattern is exactly same as in OP, try this: ls *1_1.txt.fa | while read line; do echo ${line%…
Comment: Bioinformatics startup market analysis
by
grant.hovhannisyan
★ 2.1k
good luck!
Comment: Bioinformatics startup market analysis
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gtechbio
▴ 30
Dear @juanjo75es, thank you for your input. We do agree that NGS data/metadata should be more accessible to public, in part also due to ini…
Comment: Bioinformatics startup market analysis
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gtechbio
▴ 30
Dear @grant.hovhannisyan, thank you for the advice. In fact we are already in touch with two local genomics facilities, though as you have …
Answer: No annotation peaks when running homer
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geneticatt
▴ 120
Try raising your p-value to make sure that they aren't all just being filtered out by that threshold (which seems pretty low). Edit: I may…
Comment: How to perform multiple alignment using MAFFT?
by
anikcropscience
▴ 40
It looks like the following: system(paste0("mafft --anysymbol --maxiterate 1000 Alignment_output/",GENE,".fa > ",GENE,".mafft.fa")) GE…
Comment: How to perform multiple alignment using MAFFT?
by
anikcropscience
▴ 40
Yes, I am using the following loop first in R to process all the files. This is the code that I am running first: blastn.filelist <- s…
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