Tag: flagstat

different result using minimap2 and pbmm2

Hi all! I am analysing CSS Pacbio data and each sample came from different run, in particular I have three files for each sample. I tested both pbmm2 and minimap2 to align my long reads, after getting the consensus sequences. This is the command I used to run mnimap2: minimap2…

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pjotrp/sambamba – sambamba – Genenetwork

10 years ago ​ 10 years ago ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 10 years ago ​ ​ ​ ​ ​ ​ 10 years ago 10 years ago 10 years ago ​ ​ 10 years ago ​ 10 years…

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I wonder if someone please explain what secondary, supplementary, duplicates and paired in sequencing mean in samtools flagstat

I wonder if someone please explain what secondary, supplementary, duplicates and paired in sequencing mean in samtools flagstat 0 ”194492 + 0 in total (QC-passed reads + QC-failed reads) 80 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 193804 + 0 mapped (99.65% : N/A) 194412 +…

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Samtools flagstat confusing result of a merged bam file

Hi, I am a bioinformatics student and I am struggling with an issue, I had paired-end fastq files for one sample with some low-quality bases at the end and adapter contamination, so I went and I trimmed my reads with trimmomatic, it gave me 4 files that I used for…

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Overestimation of number of reads from nanopore data (flagstat)

Same issue as mentioned on the minimap2 tool: github.com/lh3/minimap2/issues/236#issue-361097444 For example nanopore reads aligned to the host transcriptome the flagstat output is: 5953480 + 0 in total (QC-passed reads + QC-failed reads) 2961480 + 0 secondary 22696 + 0 supplementary 0 + 0 duplicates 4195469 + 0 mapped (70.47% :…

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Samtools flagstat

Samtools flagstat 1 I aligned my ONT sequencing run with minimap2, subsequently I filtered the file using samtools view -b -F 256 aln_transcriptome_sorted_6.bam -o filtered_aln_transcriptome_6.bam to end up with primary alignments only. When I run samtools flagstat on the filtered file I get the following output: 3502608 + 0 in…

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Alignment report

Alignment report 0 Hi Guys, I did alignment of R1 and R2 fastq files with reference genome using bwa mem and got bam file. Now, I want to check whether the alignment is done correctly and alignment percentage,coverage etc. I run following command: bwa mem hg19.fasta R1.fastq R2.fastq | samtools…

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Attempting to generate a bam.bai file but the output is not readable

Attempting to generate a bam.bai file but the output is not readable 1 Hi, I am new a exome sequencing, and have tried to follow tutorials on the subject. I am stuck at the samtools index stage because the output files are in a non-human readable format and I believe…

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Problem with using flagstat after bowtie2 alignment

I’m running bowtie2 to align multiple samples to one reference genome, and then run samtools flagstats to output the results. All but two samples have aligned and I’ve managed to run flagstat on them. For those two samples, when I run flagstat, I first get: [W::bam_hdr_read] EOF marker is absent….

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Doubt samtools flagstat

Doubt samtools flagstat 0 I’d like to see the percentage of how many sequences align with my decrementing sequence and I’ve come to this sample table. But wanted to know what use? The mapped (80.94% : N/A)or properly paired (0.06% : N/A) percentage? 1036193 + 0 in total (QC-passed reads…

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MAPQ (Mapping quality) of 0 for most reads from BWA-MEM2 (with no secondary alignment or other apparent reason)

Hello, I got a very weird output from BWA-mem2 – most of the reads have mapping quality of 0, even though there is no secondary alignment or anything else suspicious. I got sequencing data that was aligned with Novoalign to hg18, the data was bam files. I needed to realign…

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very low coverage when mappin genomic DNA

very low coverage when mappin genomic DNA 0 Hi all, I’m having terrible problems to map/align single end RNA files from human genome (GRCh.38). It is genomic DNA but was prepared by using a RNA library kit to preserve strand specificity. I’ve first tried STAR and Kallisto and the coverage…

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