Question: Tophat output problem
0
gravatar for amitunited0532
27 days ago by
amitunited05320 wrote:

Please help me to sort out this problem. Why showing 0.0% overall read mapping rate????

My result given below:

Reads: Input : 238477 Mapped : 2 ( 0.0% of input) 0.0% overall read mapping rate.

ADD COMMENTlink modified 27 days ago by WouterDeCoster28k • written 27 days ago by amitunited05320
1

Well, your first 2 problems are: 1) this is not a “tool” post, and 2) don’t use tophat

ADD REPLYlink written 27 days ago by jrj.healey4.2k
1

use STAR or HISAT2. Tophat is out of date.

ADD REPLYlink written 27 days ago by JJ300

I have changed this thread from a "Tool" to a "Question".

ADD REPLYlink written 27 days ago by WouterDeCoster28k

Post your code to understand what is going on.

ADD REPLYlink written 27 days ago by cpad01125.2k

$ tophat -G '/home/amit/Desktop/ngs new/archive-2010-09-27-22-25-17/genes.gtf' -o tophat16_2 bowtie2index SRR01545.fastq

ADD REPLYlink written 26 days ago by amitunited05320
  1. Is your fastq full fastq or part fastq? Reason is that this is a transcriptome assembly. If your fastq is part fastq, probably reads are in non coding regions
  2. Does your GTF file genome build match with reference genome? For eg. If your reference (fasta file) is hg19 and your annotations are recent (hg38). Annotations (CDS, Exon etc) may not match. Does chromosome ID match between reference fa and gtf?
  3. Is the index file correct? fastq file and index should belong same organism
  4. Is there reference file (fasta or fa file - genome.fa or hg19.fa or hg38.fa) in the same directory as index (bowtie2index folder)? Btw, please don't use numbers in directory names. One is supposed to supply directory path for index.
  5. Try to use tophat2 instead of tophat if tophat usage is necessary.

    $ tophat2 -o tophat16_2 -G /home/amit/Desktop/ngs new/archive-2010-09-27-22-25-17/genes.gtf bowtie2index .SRR01545.fastq

ADD REPLYlink modified 26 days ago • written 26 days ago by cpad01125.2k

Thank you for giving valuable time.

  1. Fastq file is full
  2. I have downloaded Homosapiens_UCSC_hg19.tar.gz (Approx 45.5 GB ). All files obtained after extract.
  3. Index and fastq file belong to same Organism (Homo sapiens)
  4. I have kept all file in one folder.
  5. I will try tophat2 instead tophat.

Thank you

ADD REPLYlink modified 26 days ago • written 26 days ago by amitunited05320
1

To my understanding, code seems to be fine considering above. I guess you have correct files in place and your GTF file annotations from hg19. GTF need not be in quotes.

Independently, take 5 or more reads (sequences) and blast against human genome. Check where they align. Sample your fastq ( some thing like 10%) and try to align instead of entire fastq. See if that works with tophat2.

ADD REPLYlink modified 26 days ago • written 26 days ago by cpad01125.2k
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