User: tarek.mohamed
tarek.mohamed • 230
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Posts by tarek.mohamed
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4
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... Hi,
I have six vcf files (cases vs control) that contain structural variants with variable length from nanopore sequence run. These vcf files were generated using NGMLR aligner followed by sniffle.
What is the best way/tool to compare these files?
Thanks
Tarek ...
written 3 months ago by
tarek.mohamed • 230
• updated
3 months ago by
WouterDeCoster ♦ 36k
0
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... Thanks for the reply!
This command will exclude 90% of reads at a position. Which reads will be excluded, is it a random process?
Do I have any power to select on what bases these reads will be excluded? as for example keep the reads with highest mapping quality or base quality scores?
Since the c ...
written 5 months ago by
tarek.mohamed • 230
1
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1
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... Hi,
I have a bam file includes a single gene sequence with huge coverage (> 5000X) from which I want to call snps. I have several snps previously identified in my sample which I am going to use as control to test my pipeline.
From my original bam file , I want to generate some bam files with dif ...
written 5 months ago by
tarek.mohamed • 230
• updated
5 months ago by
WouterDeCoster ♦ 36k
0
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Comment:
C: bcftools mpileup output format
... Hi
Thanks for the reply
I know about bcftools call, but I want to understand all of mpileup output because as you mentioned this will be used by bcftools call. By modifying bcftools mpileup parameters, hopefully I can call variants form the long reads sequence I have. My bam file pile (with huge de ...
written 5 months ago by
tarek.mohamed • 230
0
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647
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... Hi All,
I am trying to use modify bcftools mpileup / call to detect snps from nanopore sequence data with huger depth ( >5000X).
I need to understand the format of the mpileup shown bellow. I used position 84303804 as an example
> bcftools mpileup --skip-indels -C 0 -d 250 -r chr9:8427 ...
written 5 months ago by
tarek.mohamed • 230
0
votes
1
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307
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1
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... Dear All
What are the available tools for plotting sequence reads percent identitiy over a certain genetic locus in multiple samples.
I have Sam/bam files for some samples and I want to compare and plot percent identity for one gene across all samples ...
written 6 months ago by
tarek.mohamed • 230
• updated
6 months ago by
h.mon ♦ 23k
2
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1
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649
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1
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... Hi,
I am working with sequencing data generated by minion. I used minimap2 to align the long reads to reference human genome GRCh38. Now I want to call SNPs and indels, I have been searching for a tool that can work with bam files generated by minimap2.
1- Is there variant caller that work with fa ...
written 7 months ago by
tarek.mohamed • 230
• updated
12 weeks ago by
WouterDeCoster ♦ 36k
0
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1
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346
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1
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Comment:
C: Long DNA reads aligned
... I am trying to call SNPs and indels, but all the tools I found are compatible with bam files generated with specific aligners.
Is there a universal SNP caller that an work with minimap2. I do not want to use nanopolish since it works only with fast5 files. I am currently testing nanosv, is there any ...
written 7 months ago by
tarek.mohamed • 230
0
votes
1
answer
346
views
1
answers
Comment:
C: Long DNA reads aligned
... I used Minimap2 to align my minion reads to a reference genome. I then tried to sort it using picard but I got an error.
Why there is no sequence for this read?
$ java -jar /Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo/share/picard-2.17.0-0/picard.jar SortSam I=BC01_minimap.sam O=BC01 ...
written 7 months ago by
tarek.mohamed • 230
4
votes
1
answer
346
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1
answer
... Hi
What are the best long reads aligners?
I have dna sequencing data generated by minion. Which aligners should I use, I need to detect SNPs and indels downstream
Thanks
...
written 7 months ago by
tarek.mohamed • 230
• updated
7 months ago by
WouterDeCoster ♦ 36k
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