This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Output unmapped reads to a file when using tophat2

Hi, everyone,

I am using tophat2 for reads mapping. I know there is a--un option in bowtie2 to write unmapped reads to a file. However, I don't know if tophat2 has similar option (at least I did not find this option in the manual). Could anyone who has expertise on mapping give me a solution?

Another question I want to raise is: can I set large intron size? The default --max-segment-intron option is set to 500,000, if I increase it to 10,000,000, will this decrease speed a lot?

Thank you very much for any of your suggestions!

tophat2
• 3,470 views • link
updated by Ram Ram • written by biolab biolab

1 answer

  • Question 1. Tophat2 output has a file named unmapped.bam which contains unmapped reads, is this what you are looking for?
  • Question 2: I guess that the speed should not be affected very much, but I've never try a value such high as 10,000,000. I think that the only solution is to try and see. Sorry if this is not the answer you would like to have :).
• 0 views • link
updated by Ram Ram • written by iraun iraun

Hi airan,

Thanks a lot for your answer. For Question1, actually I did not mean unmapped.bam. I want to get a fastq file. Anyway, I can retrieve the reads ids, and then get sequences. For Question2, I agree to try it. Thanks.

• 0 views • link
updated by Ram Ram • written by biolab biolab

Log in to answer this question.

More posts like this
  • Tophat Reporting output tracks, run out of memory, how to solve?
    written by zoukai3412085 • zoukai3412085
    running log as follow: [2017-11-27 14:14:14] Beginning TopHat run (v2.1.1) ----------------------------------------------- [2017-11-27 14:14:14] Checking for Bowtie Bowtie version: 2.3.3.1 [2017-11-27 14:14:14] Checking for Bowtie index …
  • Topcoat error during resuming topcoat pipeline with unmapped reads
    written by lingling • lingling
    2016-07-25 12:00:56] Beginning TopHat run (v2.1.1) ----------------------------------------------- [2016-07-25 12:00:56] Checking for Bowtie Bowtie version: 2.2.9.0 [2016-07-25 12:00:56] Checking for Bowtie index files (genome).. [2016-07-25 12:00:56] …
  • TopHat error during aligning reads
    written by lingling • lingling
    I use tophat to analyze RNA-seq DATA on my Macbook Pro(RAM, 8GB) ,but there is an error: 2016-07-25 12:00:56] Beginning TopHat run (v2.1.1) ----------------------------------------------- [2016-07-25 …
  • RNA seq NGS data analysis
    written by poonam.bi01 • poonam.bi01
    hello I am runninh tophat for alingment the query sequence with the references genome sequences with this command and getting this error.. tophat2 -o SRR643880.sra_out …
  • tophat error help
    written by clizama • clizama
    I was running tophat using galaxy in amazon cloud and I git this error, someone can help me to fix it. ``` [2016-03-24 07:39:10] Checking …
  • Tophat --max-multihits option
    written by biolab biolab
    Dear all I have a simple question: Tophat2 has `--max-multihits` option. If I set it to one, does it mean that each read is mapped …
  • bowtie problem: cannot locate bowtie index
    written by biolab biolab
    Hi everyone, I actually have three minor questions about bowtie. I wrote a `run.sh` file as follows: ``` bowtie2-build rrna.fa rRNA bowtie2 --very-sensitive -x rRNA …
  • tophat reporting output problem
    written by pavanraaz • pavanraaz
    Hi I new to rna seq analysis, I have reference genome and tried to map reads. After running Tophat I got below error. what might …
  • question about Bowtie2 command
    written by biolab biolab
    Hi, everyone, I am running Bowtie2 to get mapped reads as well as unmapped reads. The following command gives mapped reads: bowtie2 -x rRNA -U …
  • Tophat2 output error
    written by K.Nijbroek • K.Nijbroek
    I am trying to run a basic Tophat2 command but it goes wrong somewhere. Perhaps anyone has experience with this error message? I'm running Tophat2 …