User: Likai Mao

gravatar for Likai Mao
Likai Mao30
Reputation:
30
Status:
New User
Location:
QIMR, Brisbane, Australia
Last seen:
3 years, 7 months ago
Joined:
3 years, 10 months ago
Email:
m*******@gmail.com

Posts by Likai Mao

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Reads in Unassigned_NoFeatures category produced by featureCounts
... Thanks Wei for your detailed explanation. It's very clear now. I remember I did find another 2 lines with same read name in BAM file mapped to different regions of reference genome, which should be primary alignments. ...
written 3.7 years ago by Likai Mao30
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Comment: C: Reads in Unassigned_NoFeatures category produced by featureCounts
... No worries. The related records in GTF file is as below. chr1    ENSEMBL transcript      630896  630958  .       +       .       gene_id "ENSG00000276171.1"; transcript_id "ENST00000617238.1"; gene_type "miRNA"; gene_status "NOVEL"; gene_name "AC114498.1"; transcript_type "miRNA"; transcript_statu ...
written 3.7 years ago by Likai Mao30
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Answer: A: Reads in Unassigned_NoFeatures category produced by featureCounts
... I actually used Subread (1.5.0 p1) to create the counts this time. I posted here just because I am used to it. The command line was same as the R version above: featureCounts -R -p --primary -a xxx.gtf -s 2 -o count.txt I extracted 'Unassigned_NoFeatures' lines from the output file (xxx.bam.featu ...
written 3.7 years ago by Likai Mao30
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Comment: C: Reads in Unassigned_NoFeatures category produced by featureCounts
... I extracted the two lines in the BAM file and list below. Note they are shown in "inline" format (you can scroll horizontally to see the rest of the whole lines). Same format was also used for the "bedtools intersect" output above (so there are 10 GTF fields after the beginning 6 converted BAM field ...
written 3.7 years ago by Likai Mao30
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Reads in Unassigned_NoFeatures category produced by featureCounts
... Hi, I have some paired-end RNA samples with similar number of sequenced reads. However, one of them had low number of assigned reads and high number of Unassigned_NoFeatures reads. Assigned    8,752,014 Unassigned_Ambiguity    4,523,883 Unassigned_MultiMapping    0 Unassigned_NoFeatures    49,769, ...
rsubread written 3.7 years ago by Likai Mao30 • updated 3.7 years ago by Wei Shi3.2k
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Comment: C: Run featureCounts in isoform/transcript level in Rsubread
... Thanks Wei. I tried allowMultiOverlap=TRUE and it worked! All GAPDH transcripts had high counts. I set useMetaFeatures=FALSE simply because I wanted to try the effects of this option. But somehow I didn't try allowMultiOverlap. By the way, I also tried GTF.featureType='transcript' as someone sugge ...
written 3.7 years ago by Likai Mao30
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Run featureCounts in isoform/transcript level in Rsubread
... Hi, I need transcript or isoform level counts. I tried gene level first. The result of GAPDH gene looks good: ENSG00000111640.14 35281 44063 44933 37448 41543 54689 32989 31520 23272 61452 38870 58003 22751 19844 28379 36308 27316 51177 42593 49435 35901 32326 48705 39685 35096 34391 24142 38428 30 ...
rsubread written 3.7 years ago by Likai Mao30 • updated 3.7 years ago by Wei Shi3.2k
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Comment: C: countPrimaryAlignmentsOnly=TRUE produced more counts
... Will the new version of Rsubread available on R 3.2.3? ...
written 3.8 years ago by Likai Mao30
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Comment: C: countPrimaryAlignmentsOnly=TRUE produced more counts
... Thanks a lot Wei. I will let them know. ...
written 3.8 years ago by Likai Mao30
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Comment: C: countPrimaryAlignmentsOnly=TRUE produced more counts
... Our IT department told me when they tried to update Rsubread on cluster, they had some troubles: it downloaded the same version as before, Rsubread_1.18.0.tar.gz. --- > source ("http://bioconductor.org/biocLite.R") Bioconductor version 3.1 (BiocInstaller 1.18.5), ?biocLite for help A newer v ...
written 3.8 years ago by Likai Mao30

Latest awards to Likai Mao

Popular Question 3.6 years ago, created a question with more than 1,000 views. For Reads in Unassigned_NoFeatures category produced by featureCounts
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Run featureCounts in isoform/transcript level in Rsubread
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Timeout error in kegga() using edgeR

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