User: gbdias

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gbdias30
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Posts by gbdias

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Extract entire reads, rather than aligned segments, from a SAM/BAM file
... An alternative I found is to use [seqtk][1]. It takes a list of sequence names in a file and extract the sequences from FASTA/Q. seqtk subseq in.fq name.lst > out.fq [1]: https://github.com/lh3/seqtk/ ...
written 4 days ago by gbdias30
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Comment: C: Extract entire reads, rather than aligned segments, from a SAM/BAM file
... Thank you. This strategy worked. ...
written 23 days ago by gbdias30
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Extract entire reads, rather than aligned segments, from a SAM/BAM file
... Hello, I am trying to extract long reads from the Blasr .sam output. However, I want to collect the **entire** raw reads that produced alignments, and not just the aligned segments. Is there an easy way to do this? Here is the blasr command I am using: blasr -noSplitSubreads -clipping none ...
bam sam blasr written 23 days ago by gbdias30
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Comment: C: What's the difference between WGS and RefSeq databases?
... Thank you for the explanation. What if I wanted to find all ERVs in a primate genome, for example. Knowing that most of these sequences are not annotated, the WGS is the option to go, right? I mean, the Refseq would not include non-annotated non-protein-coding sequences even if they are assembled in ...
written 20 months ago by gbdias30
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What's the difference between WGS and RefSeq databases?
... I read the Refseq documentation in the NCBI handbook but it is still not clear to me. I'm aware WGS represents all assembled contigs from a sequencing project, and Refseq supposedly has some curation... Does that mean WGS is more complete than Refseq (even if it includes a bunch of unnannotated fea ...
ncbi wgs refseq written 20 months ago by gbdias30 • updated 20 months ago by Denise - Open Targets4.2k
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Calculating RPKM/TPM for repetitive elements.
... Hey guys, The RPKM and TPM measures correct for read depth and gene lenght, and work reasonably well when dealing with single copy genes. However, what if I want to mapp transcripts to a repetitive element (e.g. transposon)? How do I calculate transcript abundance in a way that I'm able to compare ...
rpkm tpm rna-seq written 23 months ago by gbdias30 • updated 21 months ago by Biostar ♦♦ 20
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Answer: A: Local Blast Database
... You could possibly use Bioedit. Put all files in a single one and select the "Create local protein/nucleotide database". ...
written 2.2 years ago by gbdias30
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Why Bowtie2 and Lastz give so different results?
... Hey guys, I'm mapping 50 bp reads from several ChIP-seq datasets to a short reference (170bp). I want to measure the relative enrichment of this specific consensus in the different IP conditions. It's repetitive DNA so I guess it's ok to use a consensus. To do so, I used Bowtie2 (with the --end-to ...
bowtie2 alignment chip-seq lastz written 2.2 years ago by gbdias30
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Comment: C: How to obtain and compare genomic coordinates from RepeatMasker output?
... Thank you very much! This will help a lot. ...
written 2.3 years ago by gbdias30
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Comment: C: How to obtain and compare genomic coordinates from RepeatMasker output?
... Thank you very much! I reading BEDTools' documentation and it really seems to be the right tool for this task. ...
written 2.3 years ago by gbdias30

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