Tophat Singletons And Problems For Converting From Bam To Fastq · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

Tophat Singletons And Problems For Converting From Bam To Fastq

Hi all,

I'm trying to get my tophat output without singletons (I'm trying to convert the output back into fastq format so everything needs a mate) but even with both the no-mixed and no-discordant options in tophat, samtools flagstat is still identifying millions of singletons, which are then essentially discarded when converting to fastq.

Any ideas?

tophat fastq bam

• 2,071 views • link

written 13.5 years ago by bob-lowlow •

0 answers

No answers yet.

Log in to answer this question.

More posts like this

How to recreate FASTQ from BAM
written 7.7 years ago by simplitia •

Hi all I been testing a paired RNA.seq sample. I start with a paired of FASTQ files and do alignment with STAR and run STAR-Fusion. …
Problem when combine two sam file toghther
written 9.8 years ago by izzy.yichao.cai

Dear all, I am trying to combine two sam file together and subject to bedtools to convert it into bedpe file. The two sam file …
Tophat align_summary.txt and samtools flagstat accepted_hits.bam disagree
written 10.2 years ago by colin.kern

I've aligned an RNA-Seq library using Tophat, and I'm confused about the output as there seems to be some disagreement that I can't figure out. …
Missing reads in BAM to Fastq conversion
written 10.3 years ago by sergiogalvezrojas •

Hi, I am working with RNA-seq. After mapping a couple of files with paired-end data against a reference genome I have obtained a .bam file …
Mapping BAM/SAM file back to reference?!?!
written 10.8 years ago by ab.tsubaki •

Hi all So I have used BWA to align fastq files (mate pair, Illumina HiSeq) to a reference sequence. I then extracted the unmapped reads …
Selecting best RNA-seq mapping with TopHat
written 11.7 years ago by mjoyraj

After mapping my PE RNA-seq with Tophat with three different options (given below). I found the following mapping summary given below in table. **1) Without …
Tophat more multiple alignments than mapped reads?
written 11.7 years ago by bmpbowen •

I used bam2fastx to convert the unmapped.bam output from TopHat into new fastq files. Then I re-ran Tophat with those fastq files against a bacterial …
What causes tophat_reports error?
written 12.2 years ago by Bharat Iyengar

I had run tophat with following options: tophat --bowtie1 -p 6 -o CT16 -r 150 --mate-std-dev 75 --no-discordant --no-mixed --transcriptome-index Transcriptome and I get `tophat_reports` …
Converting Tophats Bam Output Back To Separate Paired End Read Fastq Files
written 13.7 years ago by bob-lowlow •

Hi all, I was wondering if anyone could offer me some advice on using paired end reads with Tophat, specifically with the output. I'm planning …
Hg19 Gene Annotation With Tophat/Cufflinks
written 15.0 years ago by Oliver

<p>Hello folks,</p> <p>I wondered about the appropriate gene annotation for finding differential expression with Cufflinks in human RNA-Seq data without finding new splice junctions (using …