Hi everyone,
I aligned my paired-end sequencing data using Bowtie2 and processed the resulting BAM files with Picard MarkDuplicates. However,...
389 results in 0.0047 seconds.
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Why Is My Uniquely Mapped Read Count in Samtools Higher Than in Bowtie2?
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Base-by-Base Gene Coverage Analysis in .bam Files Using samtools
Hi everyone!
I’m currently analyzing NGS data and am looking for advice on the best approach to calculate gene coverage on a base-by-base... -
Problem with ONT sequencing pipeline. Probably in the Samtools part
Hi everyone. I have two sets of .fastq files from two ONT sequencing runs and one of them isn't working after generating .bam files.
The... -
NGS Data Analysis
Good day, All!
Please I need help regarding my DNA-sequence analysis. I have done alignment and variant calling on my DNA sequence, and have... -
Elevate Your NGS Skills: Join Our 2024 Online Course
Hello SeqAnswers Community,
Are you ready to take your Next-Generation Sequencing (NGS) skills to the next level? We're excited to announce... -
Elevate Your NGS Skills: Join Our 2024 Online Course
Hello SeqAnswers Community,
Are you ready to take your Next-Generation Sequencing (NGS) skills to the next level? We're excited to announce... -
Bowtie2 aligner or Samtools error
Hello everyone,
I am relatively new to NGS data analysis , however I have managed to learn how to analyse RNA-seq and CHIP-seq data. I have written... -
Help with htseq -count read counts
Hello
I am doing a transcriptome analysis on Pseudomonas putida and I have been trying to do a read count using Htseq -count. The program... -
mapping quality scores in samtools view?
Hello!
I am using samtools view to map short reads (-phred33) against a reference genome.
The problem is that I don't know how to properly...Last edited by ampsevilla; 05-18-2023, 03:23 AM. -
Specify Bowtie2 to align a mate pair only to the same RefSeq
Hey everyone,
I am doing exome sequencing of multiple genes, of which some share great homology.
Some of the read pairs don't share... -
samtools v1.7 flagstat tsv output formats
I'm using samtools v1.7 flagstat command to summarize a reference alignment I've performed using paired-end data. I understand the output alright (attached),... -
Uniquely mapped reads on Bowtie with colorspace RNA-seq
Hi! I mapped RNA-seq of Synechococcus sp PCC7002 and used this code:
bowtie -p 2 -C -S SynechococcusPCC7002 SRR308187.fastq > $SRR308187.sam... -
Lose of paired-end info after samtools markdup
Hi all,
I just did some paired end ATAC-seq and I have been trying to analyse the data. I align with Bowtie, remove mitochondrial reads,...Last edited by ishtiaqueh; 04-20-2021, 04:19 PM. -
Samtools Flagstat, what is "with itself and mate mapped" mean?
Here is my flagstat output after running bwa mem on my paired end data.
25730940 + 0 in total (QC-passed reads + QC-failed reads)
... -
How to get the information of GT (genotype) field in vcf files
Hi all,
I am new to SAMtools and bcftools
. I used Hisat2 for alignment, samtools for sorting and indexing and SNP calling. Here are...
