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<prev • 1,293 results • page 1 of 44 • next >
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BAM Header for ATAC-seq
R bam atac-seq written 24 days ago by sophia.dingg • 0 • updated 6 hours ago by Biostar ♦♦ 20
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Skipping intronic locations of spliced reads (N CIGAR) in sam2tsv (jvarkit)
jvarkit bam sam2tsv written 1 day ago by kbiostars • 0 • updated 14 hours ago by Pierre Lindenbaum ♦ 129k
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How to download BAM file from VM
vm bam download written 4 days ago by nickhir • 10
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71
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Visualizing pacbio-derived alignment in IGV
alignment igv pbi bam written 11 days ago by cugopal • 0
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109
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5 follow
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How to remove reads with only Ns from bam/sam/cram file?
samtools bam cram sam remove reads written 17 days ago by erik.stricker • 0 • updated 17 days ago by Anand Rao • 300
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6 follow
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Fixing BAM file errors reported by Picard ValidateSamFile, and in featureCounts' outfile
picard featurecounts validatesamfile bam written 22 days ago by Anand Rao • 300
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Samview from bam file aligned to cDNA reference
bam sam rna-seq written 4.2 years ago by bharata1803 • 450 • updated 19 days ago by Biostar ♦♦ 20
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having trouble extracting paired reads from bam file
alignment samtools bam written 22 days ago by from the mountains • 90
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Making BAM or SAM files equivalent
alignment popoolation2 sam popoolation bam written 19 months ago by keturner123 • 0 • updated 24 days ago by Biostar ♦♦ 20
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How to selectively turn soft-clipped bases to hard-clipped bases based on part of the sequence?
clipping bam sequencing written 24 days ago by goldberry88 • 0
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109
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How to get inserted bases using pysam pileup
next-gen alignment pysam bam written 6 weeks ago by va90 • 10 • updated 29 days ago by Biostar ♦♦ 20
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Adding annotations to the bam file from the txt file
sequence samtools rna-seq bam written 4 weeks ago by ssaaren • 0 • updated 4 weeks ago by Ido Tamir ♦ 5.1k
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IGV Web App inside Flask Server
flask alignment bam igv written 12 months ago by milind_ag • 10 • updated 4 weeks ago by Jim Robinson • 280
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read and write a bam: but duplicate the quality column (11) and write one with "OQ:Z:" flag
alignment samtools base quality bam pysam written 10 weeks ago by gnanakkan • 0 • updated 5 weeks ago by Biostar ♦♦ 20
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17 follow
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Bam File: Change Chromosome Notation
bam samtools written 8.7 years ago by Lisanne • 130 • updated 5 weeks ago by sacha • 1.9k
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Filter bam files based on length of contig
assembly metagenomics bam map sam written 5 weeks ago by susheelbhanu • 0 • updated 5 weeks ago by ATpoint ♦ 36k
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1
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Issue with Duplicates reads in Exom Data
duplicates alignment bam sequencing written 6 weeks ago by Ranan Jyoti Sarma • 60 • updated 6 weeks ago by i.sudbery ♦ 8.1k
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BAM to G-PhoCS file format conversion
format conversion alignment bam g-phocs written 6 weeks ago by mrnlmishra • 0
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107
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translating a bam file to protein sequences
translate bam protein samtools written 6 weeks ago by Assa Yeroslaviz • 1.3k
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quickly getting paired-end fastq of all unmapped reads from BAM file
fastq bam samtools written 6 weeks ago by dp • 40
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Rna-Seq Split Gap Size Cutoff?
rnaseq bam written 6.8 years ago by Alex Reynolds ♦ 30k • updated 6 weeks ago by Biostar ♦♦ 20
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quality check of bam files
gatk quality bam sam written 7 weeks ago by gabri.mochales • 30 • updated 7 weeks ago by Pierre Lindenbaum ♦ 129k
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How can I input a BAM file to the samtools mpileup command without using a text file?
variant calling bam samtools mpileup written 3.3 years ago by cristian • 240 • updated 7 weeks ago by Biostar ♦♦ 20
4
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1
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131
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1
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Improve the speed of Haplotypecaller
vcf gatk haplotypecaller bam written 7 weeks ago by gabri.mochales • 30 • updated 7 weeks ago by Pierre Lindenbaum ♦ 129k
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1
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141
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Merging bam files with GATK
gatk merge bam written 7 weeks ago by gabri.mochales • 30 • updated 7 weeks ago by Pierre Lindenbaum ♦ 129k
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1
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217
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1
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Average depth/coverage before and after PCR duplicates cleanup
meandepth bam samtools markduplicates written 3 months ago by Begonia_pavonina • 20 • updated 7 weeks ago by Biostar ♦♦ 20
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107
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combining / merging overlapping reads in bam file to one in silico long read
genome assembly sequence bam overlap written 8 weeks ago by Julia • 0
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217
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1
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Big differences between two alignment tools outputs: BWA vs NanoPipe
alignment nanopipe bwa nanopore bam written 9 weeks ago by alexandru.bologa.marian • 0
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2
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129
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from BAM to BED passing cell barcodes
bed umi bam scrna barcode written 9 weeks ago by BrunoGiotti • 110
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113
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1
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strelka2 complaining about unknown chromosome, while I have removed that from bam
strelka bam variant caller written 10 weeks ago by ruhollah • 10
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