User: iraun
iraun • 3.7k
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PhD candidate at University of Oslo.
There is a distinct difference between having an open mind and having a hole in your head from which your brain leaks out. J. Randi
Posts by iraun
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... Mmmm... Can you take a look to my second edit? Why using prebuilt indexes all the weight (expression) is given to `ENST00000462494` while using own indexes is given to `ENST00000331789`? ...
written 2.7 years ago by
iraun • 3.7k
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... Yes.
So the SNP and transcript information while building the index is "very" important? I mean, we assume that the analysis performed using `genome_snp_tran` index is better than the other? ...
written 2.7 years ago by
iraun • 3.7k
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... Sorry @Devon Ryan, my question wasn't clear. See my edit. I'm thinking that maybe the difference is not that big... ...
written 2.7 years ago by
iraun • 3.7k
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... Hello!
I'm using `HISAT2` tool for mapping a `RNA-Seq PE` dataset. The reference genome I want to align against is `GRCh37 `. I have downloaded [genome_snp_tran][1] pre-built index and run hisat2. For other hand, I tried to create my own indexes using the following command:
hisat2-build -p 6 ...
written 2.7 years ago by
iraun • 3.7k
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Comment:
C: extracting Allele Read Counts
... Depending on the variant caller you are using. For some of them you will see the following two fields under `FORMAT` column:
##FORMAT=
##FORMAT= ...
written 2.8 years ago by
iraun • 3.7k
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... You can take a look to this thread: [VCF filtering by depth][1]
For other hand, [SnpSift][2] is a great tool for filtering VCF files.
In your case the command would be:
`cat variants.vcf | java -jar SnpSift.jar filter "( DP > 10)" > filtered.vcf`
[1]: https://www.biostars.org/p/184457/
...
written 2.8 years ago by
iraun • 3.7k
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... [RSeQC infer_experiment.py][1]
[1]: https://www.biostars.org/p/171298/#231982 ...
written 2.8 years ago by
iraun • 3.7k
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... In the [bam-readcount GitHub repository][1], you can clearly understand the output format:
chr position reference_base depth base:count:avg_mapping_quality:avg_basequality:avg_se_mapping_quality:num_plus_strand:num_minus_strand:avg_pos_as_fraction:avg_num_mismatches_as_fraction:avg_sum_mismatch ...
written 2.8 years ago by
iraun • 3.7k
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... `Oncotator` last version: oncotator **v1.9.1.0**
Last `data source`: [here][1]
[1]: https://personal.broadinstitute.org/lichtens/oncobeta/oncotator_v1_ds_April052016.tar.gz ...
written 3.0 years ago by
iraun • 3.7k
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... I don't get the point about what you are exactly looking for, but [bcftools][1] is always a nice option for `VCF` processing.
[1]: https://samtools.github.io/bcftools/bcftools.html ...
written 3.0 years ago by
iraun • 3.7k
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For C: searching reads with a certain sequence in fastq file
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For samtools v1.3: AD, ADF and ADR fields.
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For C: How to remove regions from a vcf file ?
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For C: Why is it absolutely necessary to filter a VCF?
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For A: GT and GL fields in VCF file
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