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User: iraun

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iraun • 3.4k
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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

<prev • 373 results • page 1 of 38 • next >
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Comment: C: HISAT2 and Stringtie: difference in Stringtie results when using pre-built index
... 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 16 months ago by iraun • 3.4k
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Comment: C: HISAT2 and Stringtie: difference in Stringtie results when using pre-built index
... 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 16 months ago by iraun • 3.4k
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Comment: C: HISAT2 and Stringtie: difference in Stringtie results when using pre-built index
... Sorry @Devon Ryan, my question wasn't clear. See my edit. I'm thinking that maybe the difference is not that big... ...
written 16 months ago by iraun • 3.4k
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HISAT2 and Stringtie: difference in Stringtie results when using pre-built indexes or creating new ones in HISAT2
... 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 ...
hisat2 written 16 months ago by iraun • 3.4k
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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 17 months ago by iraun • 3.4k
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Comment: C: how to filter vcf file based on sample DP? vcf tools does not work
... 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 17 months ago by iraun • 3.4k
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Comment: C: Strand specific pair end sequencing
... [RSeQC infer_experiment.py][1] [1]: https://www.biostars.org/p/171298/#231982 ...
written 18 months ago by iraun • 3.4k
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Answer: A: bam-readcount : Reference_base is not the base with highest count
... 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 18 months ago by iraun • 3.4k
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Answer: A: Oncotator Most Recent Version and Data Source
... `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 19 months ago by iraun • 3.4k
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Comment: C: How to preprocess, normalize, decompose a VCF file before inputting to the SNPEf
... 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 19 months ago by iraun • 3.4k

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Popular Question 16 months ago, created a question with more than 1,000 views. For GATK: HaplotypeCaller gVCF and multisample
Popular Question 18 months ago, created a question with more than 1,000 views. For GATK: HaplotypeCaller gVCF and multisample
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Question of INFO parameter (precise) in VCF
Scholar 18 months ago, created an answer that has been accepted. For A: remove part of a multifasta header with sed or other
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Question of INFO parameter (precise) in VCF
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Question of INFO parameter (precise) in VCF
Popular Question 20 months ago, created a question with more than 1,000 views. For GATK: HaplotypeCaller gVCF and multisample
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Question of INFO parameter (precise) in VCF
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Popular Question 22 months ago, created a question with more than 1,000 views. For VCF_format, a point in REF/ALT columns
Scholar 22 months ago, created an answer that has been accepted. For A: remove part of a multifasta header with sed or other
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Popular Question 2.0 years ago, created a question with more than 1,000 views. For GATK: HaplotypeCaller gVCF and multisample
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