User: pablo

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pablo150
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Posts by pablo

<prev • 150 results • page 1 of 15 • next >
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Answer: A: De novo alignement with smrttools
... Hi @SP , I first defined the cromwell.conf file with `pbcromwell configure --default-backend Local --output-file cromwell.conf` , then I used that command line `pbcromwell run pb_hgap4 -e subreadset.xml --config full/path/cromwell.conf --output-dir output_assembly` ...
written 5 days ago by pablo150
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Comment: C: How to determine coverage cutoffs in k-mer distribution
... Thanks a lot, that helps! I asked that because I used the tool `purged_dups` to improve my assembly. One step of `purge_dups` pipeline is estimating these cutoffs , stored in a file like that : `5 13 21 25 42 75` I understand the first one (5) is to remove the kmers assoc ...
written 5 weeks ago by pablo150
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How to determine coverage cutoffs in k-mer distribution
... Hello, Could someone explain me clearly why do we set cutoffs coverage in kmer distribution in order to improve assemblies? And so, how to determine these cutoffs? Best ...
assembly kmer distribution kmer written 5 weeks ago by pablo150 • updated 5 weeks ago by Mensur Dlakic8.1k
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k-mer distribution to estimate the heterozygosity of my assembly
... Hello, I had PacBio CCS reads I assembled using hifiasm/v12 . I got an assembly of 1.9Gb whereas I expected a genome of 1.3Gb, which means there is a possible high reads heterozygosity rate (this is a plant genome, which could be possible). To check that, I used GenomeScope. I got that k-mer distr ...
purge_dups assembly kmer pacbio written 5 weeks ago by pablo150
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Comment: C: Difference of transcripts between my GFF file and the IGV results
... I will install that tools. Actually, when I run `samtools inxstats my_alignment.bam` , I find the right number of reads/isoforms for the scaffold in question `Super-Scaffold_100047 379068 25 0` . Then, the problem comes from the GFF file which is bad created. ...
written 10 weeks ago by pablo150
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Comment: C: Difference of transcripts between my GFF file and the IGV results
... I updated my post as you can see with the mentioned GFF file. ...
written 10 weeks ago by pablo150
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Comment: C: Difference of transcripts between my GFF file and the IGV results
... There's not. I check each transcript : they are all unique and align only once on the genome. Also, when I count the number of transcripts specific to that scaffold in my alignment.bam file, I got 25 sequences. Do you know if there is a way to count the number of alignments with IGV? I could verif ...
written 10 weeks ago by pablo150
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Comment: C: Difference of transcripts between my GFF file and the IGV results
... Actually, these are full length transcripts obtained from PacBio sequencing. That's why they are giant. ...
written 10 weeks ago by pablo150
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Difference of transcripts between my GFF file and the IGV results
... Hi, I aligned my transcripts reads generated by the Isoseq tool, against my reference. Then, I generated a GFF file. When I look at the number of transcripts in the GFF file and with IGV, there is a difference. For example, I focus on a specific scaffold (named Super-Scaffold_100047) of the refere ...
gff transcripts igv written 10 weeks ago by pablo150
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Transcript sequence aligns twice on the reference
... Hi, I generated transcript sequences with the Isoseq3 pipeline from PacBio. Then, I aligned these sequences against my fasta reference, with `pbmm2 align` tool ; it worked well. My question is : why some of my full length transcripts (76 transcripts out of 94818) align twice (sometimes more, up ...
alignement bam written 10 weeks ago by pablo150 • updated 10 weeks ago by JC12k

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Popular Question 5 weeks ago, created a question with more than 1,000 views. For Correlation Matrix - Big Data - R
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