User: fate.gh

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fate.gh10
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Posts by fate.gh

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Comment: C: Alignment rate differes using hg19 and hg38
... Hi, Yes, These are the same exact inputs and parameters... I ran htseq-count and compared the results, but since the gtf files are different (different ensembl versions to match hg19 and hg38), the result are not the same. ...
written 2.1 years ago by fate.gh10
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Alignment rate differes using hg19 and hg38
... I have some RNA-seq fastq files.I'm using HiSat to align the fastq files. To do so, I use the built-in genome reference in Galaxy. When I align them to hg19, the alignment rate is much higher than when I align them to hg38. What causes such big difference? Here this is an example: ***** Alignment ...
alignment rate hg39 hg19 hisat written 2.1 years ago by fate.gh10 • updated 2.1 years ago by Jennifer Hillman Jackson25k
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Answer: A: How to create GFF file for HT seq
... I'm not very professional but as I know from [HTSeq 0.6.1p2 documentation ][1], In GTF files generated by the Table Browser function of the UCSC Genome Browser, the gene_id attribute incorrectly contains the same value as the transcript_id attribute and hence a different value for each transcript of ...
written 2.1 years ago by fate.gh10
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htseq read counts zero
... Hi, I have imported some fastq files (homo sapiens) from http://www.ebi.ac.uk/ena/data/ to Galaxy. In order to obtain read counts, I aligned them to hg19 using HiSat (default parameters). Then since my reference genome was hg19, I used GTF file (Version 19 (July 2013 freeze, GRCh37) - Ensembl 74, 7 ...
htseq read counts annotation rna-seq written 2.1 years ago by fate.gh10 • updated 2.1 years ago by Jennifer Hillman Jackson25k

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