User: iraun

gravatar for iraun
iraun3.7k
Reputation:
3,680
Status:
Trusted
Location:
Norway
Last seen:
1 month ago
Joined:
5 years, 7 months ago
Email:
i********@gmail.com

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 • 372 results • page 1 of 38 • next >
0
votes
0
answers
1.9k
views
0
answers
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 2.7 years ago by iraun3.7k
0
votes
0
answers
1.9k
views
0
answers
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 2.7 years ago by iraun3.7k
0
votes
0
answers
1.9k
views
0
answers
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 2.7 years ago by iraun3.7k
1
vote
0
answers
1.9k
views
0
answers
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 2.7 years ago by iraun3.7k
1
vote
1
answer
1.8k
views
1
answers
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 iraun3.7k
2
votes
0
answers
3.7k
views
0
answers
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 2.8 years ago by iraun3.7k
1
vote
1
answer
3.4k
views
1
answers
Comment: C: Strand specific pair end sequencing
... [RSeQC infer_experiment.py][1] [1]: https://www.biostars.org/p/171298/#231982 ...
written 2.8 years ago by iraun3.7k
3
votes
1
answer
731
views
1
answers
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 2.8 years ago by iraun3.7k
0
votes
1
answer
898
views
1
answers
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 3.0 years ago by iraun3.7k
0
votes
0
answers
1.2k
views
0
answers
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 3.0 years ago by iraun3.7k

Latest awards to iraun

Appreciated 2.7 years ago, created a post with more than 5 votes. For C: searching reads with a certain sequence in fastq file
Appreciated 2.7 years ago, created a post with more than 5 votes. For A: FPKM vs raw counts vs RPKM
Appreciated 2.7 years ago, created a post with more than 5 votes. For samtools v1.3: AD, ADF and ADR fields.
Appreciated 2.7 years ago, created a post with more than 5 votes. For C: Question about gens name starting "LOC~"
Appreciated 2.7 years ago, created a post with more than 5 votes. For C: How to remove regions from a vcf file ?
Appreciated 2.7 years ago, created a post with more than 5 votes. For C: Why is it absolutely necessary to filter a VCF?
Appreciated 2.7 years ago, created a post with more than 5 votes. For A: GT and GL fields in VCF file
Great Question 2.7 years ago, created a question with more than 5,000 views. For GATK: HaplotypeCaller gVCF and multisample
Good Question 2.7 years ago, asked a question that was upvoted at least 5 times. For samtools v1.3: AD, ADF and ADR fields.
Good Answer 2.7 years ago, created an answer that was upvoted at least 5 times. For A: Best software to assemble bacterial genomes
Good Answer 2.7 years ago, created an answer that was upvoted at least 5 times. For C: searching reads with a certain sequence in fastq file
Good Answer 2.7 years ago, created an answer that was upvoted at least 5 times. For A: FPKM vs raw counts vs RPKM
Good Answer 2.7 years ago, created an answer that was upvoted at least 5 times. For C: Question about gens name starting "LOC~"
Popular Question 2.7 years ago, created a question with more than 1,000 views. For GATK: HaplotypeCaller gVCF and multisample
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Get completely overlapping features
Popular Question 2.7 years ago, created a question with more than 1,000 views. For How can I know if snp is inside a protein domain?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For SGA: get the coordinates of contig scaffolding
Popular Question 2.7 years ago, created a question with more than 1,000 views. For samtools v1.3: AD, ADF and ADR fields.
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Pindel: RPL structural variation type
Popular Question 2.7 years ago, created a question with more than 1,000 views. For scaffolding denovo contigs to genome
Popular Question 2.7 years ago, created a question with more than 1,000 views. For vcf-consensus with more than one alternative alleles
Popular Question 2.7 years ago, created a question with more than 1,000 views. For check the variations incorporated to consensus fasta by vcf-consensus
Popular Question 2.7 years ago, created a question with more than 1,000 views. For bwa.kit: run-bwamem or bwa mem
Popular Question 2.7 years ago, created a question with more than 1,000 views. For How to pick simulation parameters for the RNASeqReadSimulator
Appreciated 2.7 years ago, created a post with more than 5 votes. For A: Best software to assemble bacterial genomes

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 791 users visited in the last hour