Hello everyone,
I have RNA seq data of 12 samples (paired end, so 24 files) and I ran tophat2 for alignment on all of them which gave...
57 results in 0.0025 seconds.
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splitting Tophat2 bam files in separate samples
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Very low TopHat aligment using public available dataset
Probably I'm missing something very simple, but I'm quiet new on this and maybe you can help me to sort this out.
I've downloaded a raw... -
Cuffset number of genes too high
Hi,
So I'm implementing a pretty standard tuxedo pipeline on paired-end mouse data. I went along as follows.
Using the... -
Large number of Unassigned_NoFeature reads from featureCounts
I have a bit of a mystery on my hands about an RNA-Seq Project.
I am working with some mice lines, standard RNA-seq prep, paired end. ... -
Not 100% mapping in output bam?
Running samtools flagstat on a bam file resulting from alignment with Hisat2 gives:
...Code:76075665 + 0 in total (QC-passed reads + QC-failed reads)
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HTSeq-count: Warning: x reads with missing mate encountered.
As I am running through an RNA-Seq pipeline using Hisat2 for alignment and HTSeq-count for counting reads in features I notice this warning at the bottom...Last edited by ronaldrcutler; 12-24-2016, 08:04 AM. -
Hisat2: Differing amount of reads in mates
Hello all,
I am aligning paired-end reads using Hisat2. Unfortunately, some of the fastq files were corrupted in transfer. I was able to... -
Low tophat2 mapping of paired-end reads
Hello. I'm trying to map paired-end reads on the reference scaffold using tophat2, but the percentage of mapped reads is almost 0%.
Left... -
Is there a difference between a .sam produced by tophat2 and bowtie2?
I hope this makes sense,
So I have a perl script that is written to take the accepted_hits.bam file from tophat2, in sam format as an input....Last edited by meabh; 05-24-2016, 06:51 AM. Reason: I didn't realise you could output sam file from tophat2 which makes the question redundant -
biological replicates cuffmerge?
Dear forum,
I have 5 RNA-seq biological replicates and wish to examine the expression levels of specific genes/pathways of interest (high/low/not... -
tophat2/2.1.0 error running from bam2fastx
I am running tophat2.1.0 (bowtie 2.2.6.0) on SE RNAseq data and encountering the following error:
[2016-02-29 09:38:34] Beginning... -
extract_only_concordant_paired_reads_from_bam_file
Hi everyone,
I am trying to extract only concordant paired reads from my bam file using a command that I found in posts with similar subject:... -
tophat2 aligment ratio reduced when increase insert size
Now I have two set of HiSeq pair end equencing data for the same sample with different insert size(196 and 225). The I use tophat2 to align the reads... -
Tophat2 can't find Bowtie index files *.ebwt
I have run tophat2 using cmd:
tophat2 --bowtie1 -p 6 -G /project/Ref_Genome/GRCm38.gtf -N 2 -r 40 --library-type fr-unstranded -o ./ /project/Ref_Genome/GRCm38.genome.fa... -
Mixing paired-end and single-end reads in Tophat: Do I have to reverse the SE-reads f
This is a cross-post from the Tuxedo Google group: https://groups.google.com/forum/#!to...rs/BtI3_fp_n-o
And a follow-up...
