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<div class="faq_title">
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<span>List of questions sent to refTSS help desk and answers from refTSS team<br>
 +
Between 27th January 2019- 16th June 16, 2021</span>
 +
</div>
 
<div class="menu">
 
<div class="menu">
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   <label for="item1">Q1. Is there dataset of transcription start sites collected with only noncording RNA regions?</label>
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   <label for="q1">Q1. Is there dataset of transcription start sites collected with only noncording RNA regions?</label>
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   <input type="checkbox" id="q1">
 
   <ul>
 
   <ul>
 
     <li>A1. Currently, there are no data that collects only the transcription start sites of non-coding RNAs. It is possible to extract noncording RNAs by concatenating the GENCODE annotation file and the following files:<br>
 
     <li>A1. Currently, there are no data that collects only the transcription start sites of non-coding RNAs. It is possible to extract noncording RNAs by concatenating the GENCODE annotation file and the following files:<br>
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</li>
 
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   <label for="item2">Q2. Why the range of some TSSs are so much greater than others? For most TSSs the range is in the region of 8-24 bp, while for others the range is over 100 bp.</label>
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   <label for="q2">Q2. Why the range of some TSSs are so much greater than others? For most TSSs the range is in the region of 8-24 bp, while for others the range is over 100 bp.</label>
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   <input type="checkbox" id="item2">
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   <input type="checkbox" id="q2">
 
   <ul>
 
   <ul>
 
     <li>A2. The range of TSSs is in the region of 8-24 bp, while for others the range can be over 100 bp. We computationally identify TSS regions based on the mapping results with 5'-end sequences.</li>
 
     <li>A2. The range of TSSs is in the region of 8-24 bp, while for others the range can be over 100 bp. We computationally identify TSS regions based on the mapping results with 5'-end sequences.</li>
 +
  </ul>
 +
  <label for="q3">Q3. most TSSs with an associated gene symbol are within ~20 bp of the 5' end of a known transcript, but how much confidence can we have that TSSs that are much further away than this truly represent a TSS for the associated gene? .</label>
 +
  <input type="checkbox" id="q3">
 +
  <ul>
 +
    <li>A3. We search for potential associated genes based on our annotation pipeline.
 +
In this pipeline, we searched for annotated TSS within 500 bp, and choose the nearest genes as associated ones. In this case, we consider the TSS is an unannotated (undetected) 1st exon. Of course, since it is a prediction, it can be incorrect. We have no clear guidelines about the confidence, but the distance can be a quasi-measure of the strength of the prediction.</li>
 +
  </ul>
 +
  <label for="q4">Q4. Could you please provide with more information about the GRCh38.p10 file?</label>
 +
  <input type="checkbox" id="q4">
 +
  <ul>
 +
    <li>A4. Usually, even if the patch number is different, the coordination is not changed. You can use the current TSSs coordinates provided in refTSS regardless of the patch number.</li>
 +
  </ul>
 +
  <label for="q5">Q5. How to go about making a GTF from the provided refTSS BED files?</label>
 +
  <input type="checkbox" id="q5">
 +
  <ul>
 +
    <li>A5. There are many ways in which you can convert BED file formats to GTF. For example, a command that uses UCSC tools (bedToGenePred and genePredToGtf) like this:
 +
<pre>> bedToGenePred in.bed /dev/stdout | genePredToGtf file /dev/stdin out.gtf</pre><br>
 +
If you are using Galaxy, it provides solution for converting BED to GTF.</li>
 +
  </ul>
 +
  <label for="q6">Q6. When looking at the TSS sites on your refTSS track in the UCSC Genome Browser, some appear blue and others red. Why is this difference? On the other hand, the number of white arrow heads within the TSS sites is indicative of what?</label>
 +
  <input type="checkbox" id="q6">
 +
  <ul>
 +
    <li>A6. In refTSS’ UCSC configuration of the bigBed 6 tracks, we set the option:
 +
colorByStrand 255,0,0 0,0,255
 +
 +
This setting enables to show alignments on the reverse strand colored in dark red, whereas alignments on the forward strand are colored in dark blue. Again, in refTSS UCSC configuration of the bigBed 6 tracks, we set the option:
 +
  exonArrows on
 +
exonArrowsDense on
 +
  The above options enable us to show the Exon arrows in white heads within the TSS.</li>
 +
  </ul>
 +
  <label for="q7">Q7. Does the refTSS project have bigWig file format to verify strengths of TSS peak? </label>
 +
  <input type="checkbox" id="q7">
 +
  <ul>
 +
    <li>A7. In the current release of refTSS we only provide BED and TEXT formats, but not bigWig files. We are planning to offer this in a future release. However, the BED files from refTSS can be used to generate bigwig file format using several UCSC tools (*<a href="http://hgdownload.soe.ucsc.edu/admin/exe/">http://hgdownload.soe.ucsc.edu/admin/exe/</a>) that supports this kind of conversion.</li>
 +
  </ul>
 +
  <label for="q8">Q8. Could you point me to the direction of the bed files containing TSS peak-score info, or the raw data?</label>
 +
  <input type="checkbox" id="q8">
 +
  <ul>
 +
    <li>A8. In refTSS we only integrate TSS regions, but not the TSS tag counts (Score), this is due to the fact that different data sources use different sequence specifications. Instead, we recommend you take the expression tables from the FANTOM5 web site (<a href="https://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_latest/extra/CAGE_peaks_expression/">https://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_latest/extra/CAGE_peaks_expression/</a>) and then retrieve the count data.</li>
 +
  </ul>
 +
  <label for="q9">Q9. Is there a possibility to determine the location of the translational start site and the premature stop codon according to the refTSS sequence? </label>
 +
  <input type="checkbox" id="q9">
 +
  <ul>
 +
    <li>A9. In the current version of refTSS, you can’t determine the location of the start and stop codons, but you can predict them using the transcript and protein annotation information provided by refTSS at <a href="http://reftss.clst.riken.jp/datafiles/current/mouse/gene_annotation/">http://reftss.clst.riken.jp/datafiles/current/mouse/gene_annotation/</a> </li>
 +
  </ul>
 +
  <label for="q10">Q10. Is it possible to get the cell or tissue information for the TSS regions in the database?</label>
 +
  <input type="checkbox" id="q10">
 +
  <ul>
 +
    <li>A10. In the current release of refTSS we are not providing sample information (i.e. cell or tissue etc.). If you need such info, you will need to look at the source of TSS from here <a href="http://reftss.clst.riken.jp/datafiles/current/human/sources/">http://reftss.clst.riken.jp/datafiles/current/human/sources/</a></li>
 
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   </ul>
 
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Revision as of 15:57, 18 June 2021

List of questions sent to refTSS help desk and answers from refTSS team
Between 27th January 2019- 16th June 16, 2021
  • A2. The range of TSSs is in the region of 8-24 bp, while for others the range can be over 100 bp. We computationally identify TSS regions based on the mapping results with 5'-end sequences.
  • A3. We search for potential associated genes based on our annotation pipeline. In this pipeline, we searched for annotated TSS within 500 bp, and choose the nearest genes as associated ones. In this case, we consider the TSS is an unannotated (undetected) 1st exon. Of course, since it is a prediction, it can be incorrect. We have no clear guidelines about the confidence, but the distance can be a quasi-measure of the strength of the prediction.
  • A4. Usually, even if the patch number is different, the coordination is not changed. You can use the current TSSs coordinates provided in refTSS regardless of the patch number.
  • A5. There are many ways in which you can convert BED file formats to GTF. For example, a command that uses UCSC tools (bedToGenePred and genePredToGtf) like this: 
    >	bedToGenePred in.bed /dev/stdout | genePredToGtf file /dev/stdin out.gtf

    If you are using Galaxy, it provides solution for converting BED to GTF.
  • A6. In refTSS’ UCSC configuration of the bigBed 6 tracks, we set the option: colorByStrand 255,0,0 0,0,255 This setting enables to show alignments on the reverse strand colored in dark red, whereas alignments on the forward strand are colored in dark blue. Again, in refTSS UCSC configuration of the bigBed 6 tracks, we set the option: exonArrows on exonArrowsDense on The above options enable us to show the Exon arrows in white heads within the TSS.
  • A7. In the current release of refTSS we only provide BED and TEXT formats, but not bigWig files. We are planning to offer this in a future release. However, the BED files from refTSS can be used to generate bigwig file format using several UCSC tools (*http://hgdownload.soe.ucsc.edu/admin/exe/) that supports this kind of conversion.

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