User: eozcan

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eozcan0
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Posts by eozcan

<prev • 15 results • page 1 of 2 • next >
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Comment: C: High no feature counts in ht-seq counts
... I tried another annotation file and a fasta file from Ensemle, the previous one from ncbi. In order to see if there is a problem with the annotation file. I got lower counts and higher no feature. ...
written 5 weeks ago by eozcan0
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Comment: C: High no feature counts in ht-seq counts
... I tried that it does not change/improve my reads. ...
written 5 weeks ago by eozcan0
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Comment: C: High no feature counts in ht-seq counts
... I am not sure if you can see the image. But it is aligning to the genes. ...
written 5 weeks ago by eozcan0
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Comment: C: High no feature counts in ht-seq counts
... ![enter image description here][1]does this mean they are aligning to genome? [igvsnapshot][2] [1]: http://tinypic.com/view.php?pic=mvs0b8&s=9#.XBKfahNKjfA [2]: http://tinypic.com/view.php?pic=mvs0b8&s=9#.XBKfahNKjfA ...
written 5 weeks ago by eozcan0 • updated 5 weeks ago by genomax60k
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Comment: A: High no feature counts in ht-seq counts
... [Update] my sorted bam files were name sorted and ht-seq count somehow do not like that kind of sort in my samples. So, I redo htseq count with coordinate sorted bam files, however, that did not improve the no-feature counts. I had some addition to my command line as below -o eo8_sortedcoordin ...
written 5 weeks ago by eozcan0 • updated 5 weeks ago by WouterDeCoster35k
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Comment: C: High no feature counts in ht-seq counts
... I dowloaded them both from ncbi from same genome. ...
written 5 weeks ago by eozcan0
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Comment: C: High no feature counts in ht-seq counts
... stranded option is reverse, I specified it. It is there. What else is incomplete I didnt understand? ...
written 5 weeks ago by eozcan0
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Comment: C: High no feature counts in ht-seq counts
... I made the libraries and it is stranded. ...
written 5 weeks ago by eozcan0
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Comment: C: High no feature counts in ht-seq counts
... I have not. Which genome browser would you recommend? and what should I check when I review it? ...
written 5 weeks ago by eozcan0
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High no feature counts in ht-seq counts
... Hi, I know this question has been posted before but I could not find answers to increase my counts for RNA-seq reads. I have done RNA-seq in Illumina Nextseq. I prepared libraries with NEBNext Ultra II Directional library kit. I used bowtie2 to map my reads to the reference genome. It is a bacteri ...
rna-seq sequencing written 5 weeks ago by eozcan0

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