User: morovatunc

gravatar for morovatunc
morovatunc320
Reputation:
320
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Trusted
Location:
Turkey
Twitter:
mortunco
Last seen:
19 hours ago
Joined:
1 year, 10 months ago
Email:
m*********@gmail.com

Posts by morovatunc

<prev • 169 results • page 1 of 17 • next >
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Regular Expression help for (bcf/vcf)tools filter manipulation
... Hi, I annotated the flanking regions of SNV mutations with vcftools fill-fs tool. In example; 20 10639675 . C G . . Callers=broad,dkfz,muse,sanger;NumCallers=4;VAF=0.3571;repeat_masker=L1M5;t_alt_count=25;t_ref_count=45;Variant_Classification=Intron;FS=t[C/G]c it added FS=t[C/G]c where; - ...
bcftools vcftools written 9 days ago by morovatunc320 • updated 9 days ago by Petr Ponomarenko2.3k
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Comment: C: 1000g database with wrong variant annotation?
... You can give it a try to ICGC or TCGA ? ( I see that you did not specify a sample type ). You just need to apply for the data. It contains bams, vcfs etc. ...
written 10 days ago by morovatunc320
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Answer: A: Does anybody success to download data using icgc-storage-client ?
... I have faced with the same problem before. I tried to download icgc data to my local from my local machine. Because all the data is stored in the amazon AWS cloud and you need to log-in to the AWS. Create an instance ( like a cloud machine ) and download icgc client overthere. Later on, you can use ...
written 17 days ago by morovatunc320
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Comment: C: Could you suggest me a proper feature selection method for mixed type variable d
... @Sirus thank you very much for your comment. The part where dividing data two train and test seems to confuse me a lot. Can only train my data ? and not do any prediction ?? Like a said in the question, i dont wan to predict anything. Is this possible with random forest? ...
written 29 days ago by morovatunc320
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Could you suggest me a proper feature selection method for mixed type variable data?
... Hi, We are working on cancer mutation data and we found that upon TF binding, there has been an enrichment of mutation occurrence happened on these TF binding regions. Since we couldnt a strong reason for this occurrence we wanted to use feature selection methods. We thought that say; Y ( mut ...
machine learning written 4 weeks ago by morovatunc320 • updated 27 days ago by cfay0
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Comment: C: Overlapping regions in a BedGraph file
... Hi, Is there any update about this post? Thanks. T. ...
written 5 weeks ago by morovatunc320
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Comment: C: pheatmap vs. manual hclust with different results
... you are not scaling your data when you do hclust(dist(data)). But in pheatmap, you scale your data based on column ? In pheatmap help section it says it uses hclust therefore, I think your error was caused by not giving the same input. pheatmap also have distance matrix output so check; 1) if your ...
written 5 weeks ago by morovatunc320
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Comment: C: Somatic variant call
... Have you tried giving a chance to ensemble mutation calling ? I am using ICGC cancer data for my project and I clearly see that merging passed could be very stringent. They have their own pipeline for getting a consensus from multiple callers. - 1) https://github.com/bioinform/somaticseq —> take ...
written 5 weeks ago by morovatunc320
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Transcription Factor Specific Mutation Signature Enrichment
... Hi, I am analyzing TF proximity mutations in ICGC cancer cohort and I would like to prove that upon TF binding mutation signature profile changes. When I analysed TF proximity mutation with mutations signature analysis packages (such as SomaticSignature). It gives the "the famous" signature graph ...
R mutation signature written 6 weeks ago by morovatunc320
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Comment: C: TCGA UUIDS to TCGA barcode (SampleID) in R
... Thank you. It worked for my prostate cancer RNA-seq data. ...
written 7 weeks ago by morovatunc320

Latest awards to morovatunc

Popular Question 9 weeks ago, created a question with more than 1,000 views. For HOMER find motifs from BED data
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Kallisto New RNA-seq quantification method discussion
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Visualization of Homer mergePeaks output Venn?
Voter 7 months ago, voted more than 100 times.
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Binding sites of annotated chip-seq peak files
Scholar 9 months ago, created an answer that has been accepted. For A: Binding sites of annotated chip-seq peak files
Popular Question 10 months ago, created a question with more than 1,000 views. For Kallisto New RNA-seq quantification method discussion
Centurion 12 months ago, created 100 posts.
Appreciated 13 months ago, created a post with more than 5 votes. For Kallisto New RNA-seq quantification method discussion
Supporter 18 months ago, voted at least 25 times.

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