User: Samir

gravatar for Samir
Samir140
Reputation:
140
Status:
Trusted
Location:
United States
Last seen:
5 days, 12 hours ago
Joined:
6 years, 11 months ago
Email:
s*************@gmail.com

Posts by Samir

<prev • 9 results • page 1 of 1 • next >
0
votes
1
answer
1.1k
views
1
answers
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 days ago by Samir140
0
votes
1
answer
2.3k
views
1
answers
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 5 months ago by Samir140
0
votes
1
answer
2.8k
views
1
answers
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 8 months ago by Samir140
2
votes
2
answers
11k
views
2
answers
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 8 months ago by Samir140
0
votes
2
answers
3.8k
views
2
answers
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 8 months ago by Samir140
0
votes
2
answers
3.8k
views
2
answers
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 8 months ago by Samir140
0
votes
2
answers
1.1k
views
2
answers
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 9 months ago by Samir140
8
votes
3
answers
3.9k
views
3
answers
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 3.4 years ago by Samir140 • updated 19 months ago by mforde841.2k
6
votes
12
answers
21k
views
12
answers
Answer: A: Is There Any R Or R / Bioconductor Package That Can Make Circular Plots Like Per
... Checkout OmicCIrcos at R/Bioconductor. Vignette R script provides several good examples of drawing circular plots with couple of functionalities of popular Circos software, e.g., histogram, links and ribbons, heatmap, scatterplots. ...
written 5.1 years ago by Samir140

Latest awards to Samir

Voter 3 months ago, voted more than 100 times.
Supporter 15 months ago, voted at least 25 times.
Good Answer 3.1 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 5.0 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

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2011 users visited in the last hour