User: devbt15

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devbt1510
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Posts by devbt15

<prev • 17 results • page 1 of 2 • next >
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Answer: A: FeatureCounts output does not contain all the genes in the annotation file
... Hi viDub, Unfortunately not. Since I have little time left for this work, I shifted my analysis from SubRead to Salmon based reference transcriptome analysis where I do not need the FeatureCounts or HTSeqCount. I am sorry, but I cannot help you anymore at this point in time. Regards. ...
written 3 months ago by devbt1510
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Comment: C: FeatureCounts output does not contain all the genes in the annotation file
... Here is the FeatureCounts output screenshot image for the 6 bam files as input in the code above: https://ibb.co/PFf9WxQ I also checked the read coverage for gene IDs missing from the FeatureCounts output vs annotation file. Here is the screenshot image: https://ibb.co/SmD3cK2 ...
written 4 months ago by devbt1510
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Comment: C: FeatureCounts output does not contain all the genes in the annotation file
... Thanks, I will check the bigwig on the genome browser and let you know. ...
written 4 months ago by devbt1510
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Comment: C: FeatureCounts output does not contain all the genes in the annotation file
... Yes, it is strand-specific. ...
written 4 months ago by devbt1510
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Comment: C: FeatureCounts output does not contain all the genes in the annotation file
... Yes, the names are the same. Anyways it would have been highlighted while running subread if it was not the same. ...
written 4 months ago by devbt1510
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Comment: C: FeatureCounts output does not contain all the genes in the annotation file
... Please find it here https://ibb.co/KK1kwb3 ...
written 4 months ago by devbt1510
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Comment: C: FeatureCounts output does not contain all the genes in the annotation file
... Here it is: Subread index: **subread-buildindex -F -o subreadindex ricegen.fa** Annotation file: **gffread -E riceann.gff3 -T -o riceann.gtf** Subread mapping: **subread-align -a riceann.gtf -F GTF -T 8 --sortReadsByCoordinates --multiMapping -i subreadindex -t 0 -r Q1read1.fq.gz -R Q1read2.fq.gz ...
written 4 months ago by devbt1510
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Bimodal %GC plot of fastqc output in RNASeq
... Dear all, Recently I performed RNASeq 150 bp paired-ends reads in rice (Illumina). I performed fastqc on the fastq files and obtained %GC plots (in the link below): ![enter image description here][1] As shown in the plot, a second bump is observed at 70%. However, fastqc does not suggest any overr ...
rice illumina rna-seq %gc fastqc written 4 months ago by devbt1510 • updated 4 months ago by ATpoint40k
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Comment: C: FeatureCounts output does not contain all the genes in the annotation file
... Thank you for the response. They are completely missing from the output. I also ran HTSeq-counts and it also did not provide the count data for all the genes. ...
written 4 months ago by devbt1510
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FeatureCounts output does not contain all the genes in the annotation file
... Dear all, I use Subread in Bash for mapping and FeatureCounts for count quantification for my RNASeq data. I have used the same pipeline for other RNASeq datasets in the past and FeatureCounts gives count output for all the genes in the annotation file. Recently I performed RNASeq 150 bp paired-end ...
rnaseq rice featurecounts bash written 4 months ago by devbt1510

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Popular Question 22 months ago, created a question with more than 1,000 views. For HISAT2 index creation

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