User: Samir

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Samir180
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180
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3 months, 2 weeks ago
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8 years ago
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Posts by Samir

<prev • 11 results • page 1 of 2 • next >
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Answer: A: Any Method Of Converting Bigwig File Format Into Bed Format?
... Follow up to Alex's reply, here is an example: wget http://genome.ucsc.edu/goldenPath/help/examples/bigWigExample.bw ## convert to intermediate wig format bigWigToWig bigWigExample.bw out.wig ## convert wig to bed wig2bed < out.wig > out.bed bigWigToWig executable is from ...
written 9 months ago by Samir180
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Comment: C: Retrieving Phylop Scores Using R
... Thanks for sharing details and also for phastcons in a separate post. One correction: I think there should be `--chrom $chr` option in `bedmap --echo --echo-map-score roi.perBase.bed $fn...` else it is echoing all chromosomes from roi.perBase.bed. That is strange given `$fn` only has one chromosome ...
written 12 months ago by Samir180
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Answer: A: How to detect segmental duplications?
... Look at this article and github link inside, https://academic.oup.com/bioinformatics/article/34/17/i706/5093240 Eichler lab has posted WGAC code and a detailed how-to guide at https://github.com/EichlerLab/WGAC ...
written 14 months ago by Samir180
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Comment: C: TCGA barcode documentation? TCGA wiki?
... Here is a cloned page on GDC website: https://docs.gdc.cancer.gov/Encyclopedia/pages/TCGA_Barcode/ ...
written 19 months ago by Samir180
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Comment: C: Music Analysis Workflow
... Hi Cyriac, I have mutation calls on both, set of matched tumor-normal pairs and tumor-only samples (using panel of normal approach). I doubt if music2 can be used for calling mutational significance for tumor-only samples but if you have any suggestions to do so otherwise or use comparable tools, l ...
written 21 months ago by Samir180
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Answer: A: BWA 0.7.12 and Unique reads, -r, -c options, XA: and SA: optional tags on SAM ou
... Copied from my reply at [an another forum](https://bioinformatics.stackexchange.com/a/4542/2978) *** For much faster and stable$ implementation, sambamba can handle this using following one-liner: sambamba view -t 12 -h -f bam -F "mapping_quality >= 1 and not (unmapped or secondary_alig ...
written 21 months ago by Samir180
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Comment: C: Where can I get ?or how can I make a mappability track for hg38 assembly
... Never mind and it is resolved. Somehow wig file had that extra `dna\t` in it, so I removed that first, and then was able to convert wig to BigWig. ```sh sed -i.bak -E 's/dna[\t]{0,1}//' CanFam3_1_mappability_gemlib_50.wig wigToBigWig CanFam3_1_mappability_gemlib_50.wig CanFam3_1.fa.sizes CanFam3_1_ ...
written 22 months ago by Samir180
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Comment: C: Where can I get ?or how can I make a mappability track for hg38 assembly
... Excellent script and thanks! I managed to run until the third step but wigToBigWig returned an error: *strange var=val pair line 1 of CanFam3_1_mappability_gemlib_50.wig*. I am running command: ```sh wigToBigWig CanFam3_1_mappability_gemlib_50.wig CanFam3_1.fa.sizes CanFam3_1_mappability_gemlib_5 ...
written 22 months ago by Samir180
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Comment: A: Error while downloading data from database[EGA]
... We are having similar issue with downloads failing after a prolonged wait time in downloading data from EGA servers. Using [EGA Download Client](https://www.ebi.ac.uk/ega/about/your_EGA_account/download_streaming_client#client) and following command to request and download data#### Command #Req ...
written 23 months ago by Samir180
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What is an optimal normalization approach for comparing GTEx RNASeq normal vs TCGA tumor samples?
... I am trying to compare RNA-seq read counts from normal tissue samples from GTEx to tissue-level matched TCGA tumor samples. Since TCGA has also a few normals, I am trying to merge those adjacent tissue normals (for solid tumors) with matched tissue from GTEx. While merging normals from GTEx with TCG ...
normalization sva deseq2 rna-seq written 4.5 years ago by Samir180 • updated 2.8 years ago by mforde841.2k

Latest awards to Samir

Voter 17 months ago, voted more than 100 times.
Supporter 2.4 years ago, voted at least 25 times.
Good Answer 4.2 years ago, created an answer that was upvoted at least 5 times. For A: Is There Any R Or R / Bioconductor Package That Can Make Circular Plots Like Per
Teacher 6.1 years ago, created an answer with at least 3 up-votes. For A: Is There Any R Or R / Bioconductor Package That Can Make Circular Plots Like Per

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