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...
273 results in 0.0076 seconds.
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Bowtie2 aligner or Samtools error
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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... -
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Online Course - A Practical Introduction to NGS Data Analysis
Quality Control, Read Mapping, Visualization and DNA Variant Analysis
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Bowtie: How do I map files to reference genome?
I want to map out1.fq and out2.fq to the reference genome `NC_008253.fa.fai` based on the following conditions:- - seed length=24
- hits
- - seed length=24
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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... -
Human read filtering with Kraken 2
Hey everyone,
I was wondering something regarding the usage of Kraken 2 for read filtering.
I sequence/assemble viruses and inherited...Last edited by JasperGeh; 02-04-2020, 07:02 AM. -
Tophat-fusion: Joining segment hits - FAILED
Hi,
I have been aligning RNAseq data using tophat-fusion for downstream analysis of circularRNA using CIRCexplorer2 (requires tophat-fusion... -
Bowtie-build - reference genome issue
Hello!
I`m new in NGS analysis, but in my new lab i had to replace my colleague in big NGS project related to miRNA-seq. He left me bunch... -
MapSplice2 does not recognize my Bowtie indexes
Hi everybody,
I wannted to start working with MapSplice2, however, I run into the problem that it does not recognize my Bowtie1 indexes... -
Comparing MiSeq output from different runs
Hi, I have about 4 different MiSeq runs i have data for. I have pipelined the fastq files through bowtie-samtools-cuffdiff to compare cDNA libraries of... -
Question on reads mapping smallRNA-seq (100% feature coverage)
Hi all,
I have a fastq file containing reads from an Illumina NextSeq smallRNA sequencing, a fasta file representing the genome (it is composed... -
Mapping using STAR and Bowtie
Hi all,
I want to perform an alignment of short reads against a reference genome (human genome from Ensembl). For that I've used STAR,... -
Alignment with bowtie doesn't creates .sam file
Hi,
I'm trying to align a fastq.gz file with bowtie.
My script is:
${bowtie_source} --sam --best ${ref_genome} ${fastq_file}... -
bowtie 2 dpad parameter explanation
Can someone provide a detailed explanation, what the bowtie2 parameter "--dpad" does? The explanation given in the manual is as follows: "--dpad...
