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<prev • 1,102 results • page 1 of 37 • next >
7
votes
1
answer
194
views
1
answer
Is there a way to do read filtering (MAPQ> certain value) on a BAM instead of SAM file?
quality bam sam filtering mapq written 7 weeks ago by msimmer92 • 50
0
votes
0
answers
101
views
0
answers
Getting protein fasta from RNAseq BAM file (human) paying attention on repeats
fasta repeats bam blastx rna-seq written 4 days ago by pauli.pauli • 0 • updated 4 days ago by RamRS ♦ 20k
3
votes
1
answer
101
views
1
answer
different bam from same NGS data
bam bwa written 5 days ago by gab • 20 • updated 5 days ago by jsporter • 60
0
votes
0
answers
123
views
0
answers
Help with bamfilter
sequencing blobtools bam assembly written 12 days ago by max_19 • 10 • updated 6 days ago by colindaven • 900
2
votes
1
answer
76
views
1
answer
Do the lowercase bases seen in BAM files need to be reverse complemented in consensus?
bam written 7 days ago by DNAngel • 20 • updated 7 days ago by Devon Ryan ♦ 87k
8
votes
3
answers
164
views
7 follow
3
answers
Find bams with identical names and merge them
shell picard samtools sam bam written 12 days ago by brendes • 20 • updated 10 days ago by cpad0112 ♦ 10k
4
votes
1
answer
163
views
5 follow
1
answer
losing reads bam to fastq
fixmate fastq bam whole genome sequencing written 15 days ago by soleimani_homa • 0 • updated 15 days ago by finswimmer ♦ 8.8k
86
votes
6
answers
49k
views
34 follow
6
answers
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
merge picard samtools bam written 7.5 years ago by 2184687-1231-83- • 4.9k • updated 18 days ago by mmfansler • 260
2
votes
1
answer
98
views
1
answer
Ignore SAM header section using awk
bam sam sequencing written 18 days ago by max_19 • 10 • updated 18 days ago by RamRS ♦ 20k
3
votes
2
answers
906
views
2
answers
Program to calculate and add the NM tag to a bam file
nm bam written 18 months ago by abascalfederico • 1.0k • updated 24 days ago by pammybiotech • 0
2
votes
1
answer
102
views
1
answer
Extract unmapped reads using RNAME
next-gen sequence bam written 25 days ago by max_19 • 10 • updated 24 days ago by finswimmer ♦ 8.8k
4
votes
1
answer
145
views
1
answer
Extracting Reads from paired end data in SAM file that map to a list of contig IDs
reads bam sequencing written 26 days ago by yl2019 • 10
1
vote
1
answer
118
views
1
answer
Filtering fastq vs BAM for fragment size range
bowtie2 fastq alignment bam written 28 days ago by rbronste • 230
1
vote
1
answer
135
views
6 follow
1
answer
IGV ignoring indexed and sorted .bai file and trying to create a .fai file to view an alignment
bai alignment igv fai bam written 29 days ago by cbm46672 • 0
6
votes
3
answers
2.3k
views
8 follow
3
answers
Mismatch and Indel statistics from BAM/SAM file
indel bam sam written 20 months ago by sbdk82 • 40 • updated 4 weeks ago by FatihSarigol • 110
2
votes
1
answer
201
views
1
answer
CRAM reference registry and the GRch38 reference genome
cram bam samtools variantcalling grch38 written 4 weeks ago by Mehulsharma.253 • 10 • updated 4 weeks ago by h.mon ♦ 22k
183
votes
9
answers
76k
views
162 follow
9
answers
Tutorial: How to download raw sequence data from GEO/SRA
geo sra fastq tutorial download bam written 4.4 years ago by Obi Griffith ♦ 17k • updated 4 weeks ago by Renesh • 1.5k
2
votes
0
answers
171
views
0
answers
How to recreate FASTQ from BAM
bam rna-seq sequencing written 5 weeks ago by simplitia • 30 • updated 5 weeks ago by ctseto • 20
19
votes
1
answer
742
views
1
answer
Tool: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMtools for processing SAM/BAM files
bam sam sort markduplicates bqsr tool written 12 weeks ago by Charlotte.Herzeel • 130
0
votes
1
answer
164
views
5 follow
1
answer
Extracting the full read ID when converting from BAM -> FASTQ
fastq bam samtools bwa written 5 weeks ago by ttmigueltt • 0 • updated 5 weeks ago by toralmanvar • 730
0
votes
0
answers
138
views
0
answers
Stop GATK MergeBamAlignment from unmapping reads
gatk4 gatk alignment bam mergebamalignment written 5 weeks ago by ttmigueltt • 0 • updated 5 weeks ago by finswimmer ♦ 8.8k
8
votes
2
answers
151
views
7 follow
2
answers
samtools: splitting a bam file putting all scaffolds together
splitting bam samtools scaffold written 5 weeks ago by Fedster • 20 • updated 5 weeks ago by finswimmer ♦ 8.8k
7
votes
2
answers
323
views
6 follow
2
answers
How to retain SEQ and QUAL fields in BAM file after filtering?
bam samtools bwa written 6 weeks ago by toddknutson • 50 • updated 5 weeks ago by Pierre Lindenbaum ♦ 116k
1
vote
1
answer
127
views
1
answer
gatk HaplotyperCaller bam reference
haplotypercaller gatk bam written 6 weeks ago by Peter Chung • 70
0
votes
0
answers
97
views
0
answers
RSEM BAM outputs, which one to use for RSeQC?
bam star rsem rseqc written 6 weeks ago by Freek • 10
5
votes
1
answer
1.2k
views
1
answer
Extracting tlen From BAM File Using htsjdk
htsjdk bam samtools sam tlen written 2.3 years ago by Hakan.Erol.HE • 10 • updated 6 weeks ago by Biostar ♦♦ 20
0
votes
0
answers
101
views
0
answers
diffrence between number of reads in fastqc reports and collectalignmentsummarymetrics of Picard
reads picard bam fastqc written 6 weeks ago by kk.mahsa • 80
2
votes
2
answers
172
views
2
answers
Making BAM or SAM files equivalent
alignment popoolation2 sam popoolation bam written 6 weeks ago by keturner123 • 0 • updated 6 weeks ago by finswimmer ♦ 8.8k
4
votes
0
answers
231
views
0
answers
what is the easiest/fastest way to convert from BAM to GTF
gtf bam written 3 months ago by Sam • 80 • updated 6 weeks ago by Biostar ♦♦ 20
2
votes
3
answers
124
views
3
answers
how to identify disease variants from bam file ?
atacseq vcf bam disease variants written 7 weeks ago by masaver • 0 • updated 7 weeks ago by Garan • 540
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