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Showing : SAMTOOLS • reset
199
Votes
24
Replies
139k
Views
How To Filter Mapped Reads With Samtools
samtools
7.6 years ago
sohadb1357 • 500 • updated 11 months ago
ibseq12 • 0
0
Votes
4
Replies
265
Views
samtools fixmate: Couldn't write to output file: Broken pipe
alignment samtools bwa sed
14 months ago
Ric • 240 • updated 11 months ago
Biostar 20
9
Votes
8
Replies
205
Views
Divergent number of replicates between FastQC and samtools
fastqc STAR samtools
12 months ago
user31888 • 60 • updated 12 months ago
i.sudbery 4.7k
5
Votes
5
Replies
179
Views
How to parse BAM files without requiring huge memory?
software error sequence samtools
12 months ago
kimon.frousios • 20
2
Votes
4
Replies
141
Views
Extract target region sequence with samtools but the output contains suquence exceeding the bed region
bed samtools
12 months ago
xusijiamed • 0 • updated 12 months ago
i.sudbery 4.7k
0
Votes
1
Reply
140
Views
CIGAR inconsistency BWA/GATK
bwa samtools genome sequence alignment
12 months ago
ncoca • 0
5
Votes
10
Replies
166
Views
.sra to bam conversion results in a "< myfile > does not have BAM or CRAM format error"
SRA-toolkit samtools deeptools
12 months ago
jordi.planells • 70 • updated 12 months ago
genomax 68k
0
Votes
1
Reply
177
Views
Merging BAM file with Samtools
samtools merge BAM
12 months ago
seta ♦ 1.2k • updated 12 months ago
Devon Ryan 90k
24
Votes
6
Replies
49k
Views
Merging Bam Files
picard samtools
8.4 years ago
Tryingtogetthere • 170 • updated 12 months ago
abhijit.synl • 50
0
Votes
0
Replies
95
Views
Samtools mpileup with 10x data
mpileup samtools
12 months ago
lali1 • 0
3
Votes
1
Reply
117
Views
Unexpected characters at consensus fasta generated by mpileup
samtools mpileup consensussequence
12 months ago
gokberk • 30
4
Votes
14
Replies
217
Views
How to sort sam file using shell script?
samtools sort sam file Forum
12 months ago
gerrybio2010 • 0 • updated 12 months ago
Bastien Hervé 4.2k
5
Votes
5
Replies
1.9k
Views
samtools flagstat result is different from samtools view result
SAMtools
4.2 years ago
Louis Kok • 10 • updated 12 months ago
macielrodriguez2 • 10
3
Votes
2
Replies
116
Views
report every base in a bam using bed as input
samtools bcftools
12 months ago
bioguy24 • 190 • updated 12 months ago
Pierre Lindenbaum 120k
0
Votes
5
Replies
156
Views
MarkDuplicates: Mates are missing
rna-seq trimmomatic Hisat2 picardtools samtools
12 months ago
swarajgaikwad15 • 0
3
Votes
8
Replies
484
Views
Generating consensus sequence from bam file
genome samtools bwa fasta
15 months ago
chparada • 0 • updated 12 months ago
guillaume.rbt • 590
1
Vote
3
Replies
114
Views
How can bam file only retain potential variants?
bwa sam samtools
12 months ago
gerrybio2010 • 0
0
Votes
3
Replies
1.7k
Views
How to generate vcf using samtools Version: 0.1.19-96b5f2294a?
samtools vcf ubuntu
13 months ago
Vijay Lakhujani 4.1k
5
Votes
4
Replies
224
Views
HISAT2 output direct to bam
RNA-Seq samtools
13 months ago
Adrian Pelin ♦ 2.3k • updated 13 months ago
ATpoint 17k
3
Votes
5
Replies
189
Views
Loss of reads during realignment bam
gatk bwa wgs fastQValidator samtools
13 months ago
mb2subi • 0
0
Votes
1
Reply
158
Views
Calling haploid consensus sequence from vcf
vcf samtools bcftools consensus haploid
13 months ago
philodendron • 0 • updated 13 months ago
Kevin Blighe 43k
5
Votes
3
Replies
5.0k
Views
Problems When Calling Snps Using Samtools Mpileup
samtools snp calling
7.5 years ago
玄 • 20 • updated 13 months ago
Biostar 20
0
Votes
1
Reply
144
Views
Samtools mpileup - Sudden decrease of coverage at homopolymer regions
samtools mapping mpileup
13 months ago
Louis Kok • 10 • updated 13 months ago
Kevin Blighe 43k
1
Vote
5
Replies
316
Views
SNP calling with SAMtools on multiple samples
SNP samtools vcf bam
14 months ago
madeira.ag • 0 • updated 13 months ago
Begali • 0
1
Vote
7
Replies
259
Views
mpileup format to vcf
next-gen snp samtools
13 months ago
AGE • 20
12
Votes
7
Replies
2.7k
Views
Trying To Pull Regions From An Online Bam File Without Downloading
samtools igv bam
7.9 years ago
Wjeck • 480 • updated 13 months ago
Biostar 20
0
Votes
3
Replies
203
Views
count reads mapped to multiple locations only once
bwa alignment samtools multiple mapping
13 months ago
snishtala03 • 10
1
Vote
1
Reply
248
Views
samtools stats result different from samtools flagstat
samtools
13 months ago
snishtala03 • 10
0
Votes
2
Replies
164
Views
samtools sort: truncated file. Aborting
samtools alignment picard
14 months ago
m.t.lorenc • 0
0
Votes
3
Replies
168
Views
bowtie2 piped to samtools created many samtools.tmp.bam files, how to get the single .bam file?
alignment sort bowtie2 samtools
14 months ago
dongchenchen • 10 • updated 14 months ago
h.mon 25k
9
Votes
7
Replies
272
Views
Samtools segmentation fault when extracting exons from bam file.
rna-seq alignment seg fault samtools
14 months ago
jstevenson2256 • 10 • updated 14 months ago
Damian Kao 15k
0
Votes
3
Replies
183
Views
How to find all the region where one read is mapped in a bam file
NGS SAMTOOLS DNA Mapping sequencing
14 months ago
prasoongama • 0 • updated 14 months ago
WouterDeCoster 39k
0
Votes
2
Replies
274
Views
bcftools / samtools, which database does the MAF function use?
bcftools samtools MAF
14 months ago
Davide Chicco • 80 • updated 14 months ago
Pierre Lindenbaum 120k
1
Vote
4
Replies
255
Views
Filtering BAM file to include PE reads that did not map, even though their mate did
BAM samtools filter mapping read
14 months ago
nute11a • 0 • updated 14 months ago
Istvan Albert 80k
0
Votes
0
Replies
120
Views
Variant Calling between Microbial Populations
Variant snp calling populations samtools
14 months ago
gabriel.jabud • 0
0
Votes
2
Replies
206
Views
How to get output with read counts and read count percentages from bam file?
read counts bam samtools picard
14 months ago
bayramliaziz • 0 • updated 14 months ago
WouterDeCoster 39k
7
Votes
19
Replies
908
Views
Error with samtools rmdup
ChIP-Seq samtools
2.2 years ago
Bella_p • 50 • updated 14 months ago
Biostar 20
0
Votes
7
Replies
191
Views
Bcftools Call method not detecting single nucleotide deletions?
bcftools samtools variant variant calling
14 months ago
kennyworkman • 0
1
Vote
1
Reply
152
Views
Replace @RG group by the one of another BAM
samtools addreplacerg
14 months ago
da.de • 0 • updated 14 months ago
RamRS 21k
0
Votes
1
Reply
167
Views
How many SNPs I should expect to see in a normal human embryonic stem cell (hESC) with WES analysis?
SNP hESC WES samtools
14 months ago
maria2019 • 30
1,233 results • Page 1 of 31
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Answer: How to deal with the .sra.vdbcache files after downloading a sra file? by ford • 0
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and another one....
Comment: How to install CRISPRCasFinder under Ubuntu without having administrator rights? by Michael 100
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Just delete.
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