User: Samir

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Samir170
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170
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7 years, 4 months 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 7 weeks ago by Samir170
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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 4 months ago by Samir170
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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 6 months ago by Samir170
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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 11 months ago by Samir170
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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 13 months ago by Samir170
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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 14 months ago by Samir170
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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 14 months ago by Samir170
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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 14 months ago by Samir170
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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 15 months ago by Samir170
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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 3.9 years ago by Samir170 • updated 2.1 years ago by mforde841.2k

Latest awards to Samir

Voter 9 months ago, voted more than 100 times.
Supporter 20 months ago, voted at least 25 times.
Good Answer 3.6 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 5.5 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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