User: tarek.mohamed
tarek.mohamed • 180
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Posts by tarek.mohamed
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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 14 days ago by
tarek.mohamed • 180
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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 15 days ago by
tarek.mohamed • 180
• updated
15 days ago by
WouterDeCoster ♦ 32k
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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 20 days ago by
tarek.mohamed • 180
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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 20 days ago by
tarek.mohamed • 180
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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 weeks ago by
tarek.mohamed • 180
• updated
6 weeks ago by
h.mon ♦ 19k
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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 8 weeks ago by
tarek.mohamed • 180
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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 8 weeks ago by
tarek.mohamed • 180
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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 8 weeks ago by
tarek.mohamed • 180
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... 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 9 weeks ago by
tarek.mohamed • 180
• updated
9 weeks ago by
WouterDeCoster ♦ 32k
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... Thanks for the reply !
It was really helpful ...
written 11 weeks ago by
tarek.mohamed • 180
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