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Showing top results for tag: CRAM • reset
0
votes
1
reply
334
views
Convert CRAM to BAM in pysam
python pysam BAM CRAM
updated 6 weeks ago by 20k • written 6 weeks ago by ▴ 920
5
votes
9
replies
2.4k
views
6 follow
Noob question. Samtools says my CRAM from Nebula is wonky, what can I do?
CRAM Nebula samtools
updated 6 weeks ago by ★ 1.3k • written 2.1 years ago by ▴ 70
1
vote
6
replies
616
views
Need to split a cram file into smaller pieces - how to extract and save cram format to a new file?
samtools CRAM
updated 10 weeks ago by ★ 1.3k • written 12 weeks ago by ★ 2.4k
0
votes
6
replies
623
views
from CRAM to fastq
FASTQ WGS CRAM
updated 5 months ago by 85k • written 5 months ago by • 0
0
votes
5
replies
609
views
A question about reference genome for creating the consensus sequence
fasta fa cram genome
5 months ago by me • 0
0
votes
0
replies
191
views
how to downlad slices of CRAM fro ICGC ARGO
icgc samtools cram
5 months ago by Javier • 0
3
votes
5
replies
799
views
Converting CRAM to FastQ
GATK samtools cram SamToFastq fastq
6 months ago by Maverick ▴ 10
0
votes
4
replies
505
views
Questions about transfering wgs file to reference genome file
fasta cram genome
6 months ago by me • 0
0
votes
1
reply
428
views
How to calculate depth of coverage and applying read depth filter
Depth-of-Coverage CRAM WGS
updated 7 months ago by 44k • written 7 months ago by • 0
0
votes
1
reply
301
views
Issues With Cram -> Fastq from GTEx v8 WGS
fastq GTEx cram
updated 7 months ago by 164k • written 7 months ago by • 0
1
vote
2
replies
559
views
BAM to CRAM and BAM recover with smaller size
BAM samtools CRAM
updated 7 months ago by ★ 1.3k • written 7 months ago by ▴ 390
4
votes
5
replies
1.2k
views
Any ways of extracting and filtering read sequences from cram files with samtools?
samtools cram reads sequence
7 months ago by sacryt • 0
0
votes
7
replies
920
views
Trying to extract .cram file read sequences into array
CRAM pysam reads samtools
8 months ago by sacryt • 0
10
votes
12
replies
2.4k
views
Tool: PanDepth, an ultra-fast and efficient genomic tool for coverage calculation
bam paf depth cram coverage
8 months ago by Huiyang ▴ 190
2
votes
6
replies
1.0k
views
CRAM file version
cram
updated 10 months ago by 44k • written 10 months ago by ▴ 130
5
votes
4
replies
812
views
Filter out ALT contigs from CRAM
CRAM
updated 11 months ago by 101k • written 11 months ago by ★ 2.9k
2
votes
14
replies
1.8k
views
How to slice a CRAM file into the 50kb regions padded with 1kb?
GATK BED CRAM WGS
updated 11 months ago by 85k • written 12 months ago by • 0
1
vote
7
replies
1.2k
views
Samtools filtering based on PNEXT
CRAM filtering samtools SAM BAM
updated 12 months ago by 101k • written 12 months ago by ★ 2.0k
0
votes
1
reply
400
views
Does GATK SetNmMdAndUqTags reduces the size of a CRAM?
CRAM WGS sam GATK SetNmMdAndUqTags
updated 12 months ago by 164k • written 12 months ago by • 0
1
vote
3
replies
865
views
Quantify gene expression from CRAM file
Hartwig RNA-Seq CRAM
12 months ago by wenbinm ▴ 40
0
votes
5
replies
931
views
Deepvariant and input CRAM files
Deepvariant CRAM
updated 14 months ago by 146k • written 15 months ago by ▴ 20
0
votes
0
replies
503
views
Merged CRAM output
warning samtools CRAM merging
16 months ago by Matteo Ungaro ▴ 100
3
votes
2
replies
939
views
Tool: Launched: Genozip 15 with co-compression of BAM and FASTQ
BAM CRAM compression FASTQ
updated 16 months ago by ▴ 450 • written 16 months ago by ▴ 230
5
votes
4
replies
1.6k
views
Merging CRAM files
samtools CRAM
updated 16 months ago by ★ 1.3k • written 16 months ago by ▴ 100
5
votes
4
replies
922
views
How to Split 3000 WGS CRAM files into 1Mbp length chunks
CRAM
updated 17 months ago by ★ 3.9k • written 17 months ago by • 0
1
vote
0
replies
950
views
Best Practices for CRAM <-> BAM
sambamba bam cram samtools
updated 18 months ago by 146k • written 18 months ago by ▴ 90
3
votes
3
replies
1.0k
views
converting cram to ubam
cram
19 months ago by joe_genome ▴ 50
5
votes
2
replies
735
views
find tandem repeats in DNA from CRAM/VCF file
repeats CRAM tandem VCF
21 months ago by anubratadas ▴ 20
0
votes
6
replies
1.4k
views
The most efficient way to take several random reads from CRAM file?
sequencing reads CRAM
updated 23 months ago by 101k • written 23 months ago by ▴ 20
1
vote
9
replies
1.3k
views
Quality scores of base recalibrated Cram file
fastq cram
22 months ago by asalimih ▴ 60
0
votes
4
replies
1.3k
views
Convert a cram file to fasta
cram fasta samtools
updated 16 months ago by 44k • written 2.2 years ago by • 0
0
votes
4
replies
785
views
How to trim the length of reads in a CRAM file?
cram samtools
updated 16 months ago by 44k • written 2.2 years ago by • 0
2
votes
2
replies
757
views
cram to fastq
cram fastq
updated 2.3 years ago by 85k • written 2.3 years ago by ▴ 10
5
votes
2
replies
666
views
find function with samtools - convert format to all subfolders
cram bam samtools
updated 16 months ago by 44k • written 2.5 years ago by ▴ 260
3
votes
4
replies
1.0k
views
correct fastq files for the expression analysis
cram
updated 2.8 years ago by 21k • written 2.8 years ago by ▴ 260
6
votes
10
replies
3.0k
views
Extract a gene region from a whole genome cram file from 1000 genomes
samtools cram bam
2.9 years ago by michael.flower.14 ▴ 200
3
votes
7
replies
2.0k
views
Best Omic file compressor?
cram genozip gzip compression
2.9 years ago by matthew.pace ▴ 60
2
votes
3
replies
1.2k
views
Replacing BAM with CRAM Files
CRAM
updated 3.1 years ago by 20k • written 3.1 years ago by ▴ 50
3
votes
5
replies
3.9k
views
CRAM to BAM using SAMTOOLS
SAMTOOLS CRAM BAM
updated 3.2 years ago by 164k • written 3.3 years ago by • 0
0
votes
0
replies
654
views
Nebula .cram to .bam via samtools
bam analysis cram samtools
3.3 years ago by christian.palmer • 0
1
vote
7
replies
7.5k
views
samtools, convert BAM to CRAM
samtools cram bam
updated 3.3 years ago by 85k • written 3.3 years ago by ▴ 10
0
votes
4
replies
1.6k
views
Converting multiple cram files to fastq files.
cram fatsq
updated 3.3 years ago by 44k • written 3.3 years ago by • 0
1
vote
2
replies
948
views
Get by-strand base counts at position from cram file
igv cram count strand details
3.4 years ago by davenomiddlenamecurtis ▴ 20
0
votes
1
reply
1.0k
views
Pysam and CRAM file
cram pysam samtools
updated 3.4 years ago by ★ 1.3k • written 3.5 years ago by ▴ 30
8
votes
9
replies
6.6k
views
8 follow
Issue With CRAM -> BAM -> FASTQ Conversion
samtools fastq cram bam view
updated 18 months ago by • 0 • written 5.3 years ago by ▴ 20
0
votes
2
replies
690
views
extract split-read from bam/cram file
bam cram split-read soft clip
3.7 years ago by obaid_lama • 0
10
votes
4
replies
8.2k
views
Converting CRAM to BAM without reference fasta
samtools BAM CRAM
3.7 years ago by Ld_60 ▴ 80
0
votes
0
replies
732
views
convert bam to cram with non-local reference fasta
samtools cram
3.8 years ago by Ana ▴ 200
1
vote
7
replies
1.6k
views
Read name not stored in CRAM file. Is it possible to create new read names for remapping?
cram bam samtools sequencing
updated 4.0 years ago by ★ 1.3k • written 4.0 years ago by • 0
3
votes
8
replies
3.2k
views
Extract bed regions from CRAM files
BAM CRAM
4.1 years ago by MAPK ★ 2.1k
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