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• Commandline Bowtie2 and variant call help.
  Hello there! When you run bowtie2 to align the reads to the genome, some stats about the file ar...
• HiSAT2 Alignment Rate Dropping with Cufflinks export option enabled
  I am trying to take trimmed and qc filtered paired RNA seq data and run it through HiSat2 > St...
• Filtering BAM files from HISAT2
  Hi. I am new to rna-seq and I have a couple of quick questions. My input was paired-end non-stran...
• Low alignment for paired end reads using HISAT2
  Hello, I am new to processing and analysis of RNAseq data. I have recently completed a paired-en...
• Trimmomatic output results in extremely low alignment using bowtie2
  Hello, I have trimmed by paired end data RNA seq (Illumina Miseq) data using trimmomatic. Howeve...
• BWA error [bwa_aln] 17bp reads: max_diff = 2
  I wish to align single end fastq sample using "Map with BWA" tool. The reads were trimmed several...
• Number Of Mismatches Allowed In The Initial Read Mapping
  Dear All, I tested how to set the "Number of mismatches allowed in the initial read mapping" a...
• Mapping (with HISAT2 / Bowtie) on custom genomes yields always 0 matches
  Hi, I've the following problem. I'm using HISAT2 and Bowtie. I'm using a gene with 1200 nucleoti...
• Alignment rate differes using hg19 and hg38
  I have some RNA-seq fastq files.I'm using HiSat to align the fastq files. To do so, I use the bui...
• >90% aligned concordantly 0 times ChIP-seq Bowtie2
  Hi, I know this question have raised many times here and in other forums but I've tried everythi...
• Where to find Bowtie2 output stderr filehandle?
  Dear all, I want to find the alignment rate as suggested in bowtie2 "standard error" ("stderr") ...
• Extract aligned exactly 1 time fron Bowtie2?
  I have an output from Bowtie2 aligner as below: 16075710 reads; of these: 16075710 (100...
• Visualizing BigWig is UCSC genome browser: link not available
  I wish to visualize some bigwig files generated from bamCoverage tools in the UCSC genome browser...
• bowtie2 generates a fatal error
  Hi, I am trying to map 6 fastq file using bowtie2. Some of the jobs are completed but some of th...
• Error using stringtie - AttributeError: 'NoneType' object has no attribute"
  Hi, I have **RNA-seq data** and I am interested in whole gene expression results but also transcr...
• BOWTIE BAM file alignments
  I prepared a small RNA (28-34nt) library made up of ribosome protected RNA fragments.  I prepared...
• Low mapping of paired-end reads with tophat2
  Hello. I'm trying to map paired-end reads on reference scaffold using tophat2. But the percentage...
• TopHat Align Summary - whats a good results
  Howdy, Just got the results back from top hap - looked at align summary Not sure how to read it...