Question: What tool for reads alignment are prefereble for wavClusteR input bams?
0
gravatar for alexandr.gopanenko
2.6 years ago by
alexandr.gopanenko20 wrote:

Hello everyone!

I want to analyze my PAR-CLIP data utilizing wavClusteR. So when I try to create count table from my bam file (prepared by CLC WB) by command below

countTable <- getAllSub( Bam, minCov = 10 )

I have the error like that:

Error in { : 
  task 1 failed - "solving row 140: range cannot be determined from the supplied arguments (too many NAs)"

My bam:

> Bam
GRanges object with 872714 ranges and 2 metadata columns:
             seqnames           ranges strand |                    qseq          MD
                <Rle>        <IRanges>  <Rle> |          <DNAStringSet> <character>
       [1]       chr1 [ 57283,  57298]      + |        CAGTCATTCCGAACAA          16
       [2]       chr1 [ 57283,  57298]      - |        CAGTCATTCCGAACAA          16
       [3]       chr1 [612758, 612776]      + |     CCGGAGGCTGAGGTGGGAG          19
       [4]       chr1 [612758, 612776]      - |     CCGGAGGCTGAGGTGGGAG          19
       [5]       chr1 [629167, 629204]      + | ATTATTATAA...CAATCTTCCT       19T18
       ...        ...              ...    ... .                     ...         ...
  [872710] KI270751.1   [39996, 40045]      - | CAGGTCGCTG...AGAAAGGGAC          50
  [872711] KI270751.1   [64988, 65049]      + | TTTCTGACCT...AGACGTAAAC        55A6
  [872712] KI270751.1   [64988, 65049]      - | TTTCTGACCT...AGACGTAAAC        55A6
  [872713] KI270756.1   [45603, 45618]      + |        TCCGTTCCACTTTATT         9T6
  [872714] KI270756.1   [45603, 45618]      - |        TCCGTTCCACTTTATT         9T6
  -------
  seqinfo: 524 sequences from an unspecified genome; no seqlengths

I tried to realignment my fastq files using Tophat2, Bowtie2 nevetheless I have the same error.

Can you recommend the align tools and the exact parameters I need to use to get acceptable for wavClusteR bam files.

 

Thank you in advance,

Alexandr Gopanenko

 

 

wavcluster • 442 views
ADD COMMENTlink modified 2.6 years ago by federico.comoglio100 • written 2.6 years ago by alexandr.gopanenko20
Answer: What tool for reads alignment are prefereble for wavClusteR input bams?
0
gravatar for federico.comoglio
2.6 years ago by
Switzerland
federico.comoglio100 wrote:

Hi Alexandr,

thank you for your interest in wavClusteR. Can you please let me know about the exact nature of your fastq data? Is this a paired-end run? In principle, the choice of the aligner does not matter as long as gaps are not allowed and reads are single-end. wavClusteR has been thoroughly tested with bowtie, but I'm aware of some users who employed different aligners for pre-processing.

Hope this helps.

Federico

ADD COMMENTlink written 2.6 years ago by federico.comoglio100
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