User: aindap

gravatar for aindap
aindap120
Reputation:
120
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Trusted
Location:
United States
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Google Scholar Page
Last seen:
2 weeks ago
Joined:
8 years, 4 months ago
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i*****@gmail.com

I'm a tall drink of water. I like human genetics, Python, swimming, and the Phoenix Suns.

Posts by aindap

<prev • 17 results • page 1 of 2 • next >
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Answer: A: Hisat2 error: --read-lengths arg must be at least 20
... Oooof - this is what happens when you try and do work late at night and exhausted. Yes, I does seem some sequences in my fastq(s) were not minimum length. I will have to filter for length before running. Problem solved. Thanks for your reply. ...
written 7 weeks ago by aindap120
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Hisat2 error: --read-lengths arg must be at least 20
... I am new to Hisat2 and I am trying to align paired-end rnaseq fastq files with hisat2 v 2.2.0. I downloaded the hg38 transcriptome index from the software [homepage][1]. My command is: hisat2 -x genome_tran -p 8 -1 1.fastq.gz -2 2.fastq.gz | samtools view -bS - > hisat2.bam I get the f ...
alignment rna-seq written 7 weeks ago by aindap120 • updated 15 days ago by sifanye19970
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Answer: A: finding contigs present in one assembly but missing from another
... Have you tried [Assemblytics][1]? You can use [Mummer][2] to align your two assemblies and then use Assemblytics to see the differences. [1]: http://assemblytics.com/ "Assemblytics" [2]: http://mummer.sourceforge.net/ ...
written 2.4 years ago by aindap120
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GeneSCF and P-value Benjamini and Hochberg (FDR)
... Dumb question about the GeneSCF output. If I'm using the P-value Benjamini and Hochberg (FDR) column, would I choose an FDR cut point and take any rows with a BH P-value less than this value as significant? Thanks so much. ...
genescf written 2.8 years ago by aindap120 • updated 2.8 years ago by EagleEye6.6k
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Error correcting PacBio reads prior to alignment with bwa mem
... I have PacBio reads of my organism of interest that I would like to align to a reference sequence pulled from GenBank. Does it make sense to error correct and trim the PacBio reads, with a tool like [canu][1] and then align with bwa mem? [1]: http://canu.readthedocs.io/en/latest/index.html ...
bwa pacbio written 3.2 years ago by aindap120 • updated 3.2 years ago by Charles Warden7.7k
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Aligning de-novo assembly to reference strain genome
... Dear Biostars Community - I generated a de-novo assembly of my viral strain. I wanted to analyze differences of my denovo result to a reference strain, so got a very useful report from [Assemblytics][1] in conjunction with using the [nucmer][2] program from MUMmer. However the output of the alignme ...
multiple sequence alignment denovo assembly written 3.3 years ago by aindap120 • updated 2.6 years ago by asur0
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Comment: C: denovo-assembly with novel genes inserted
... Thank you so much!!! tadpole worked much *faster* and I got longer contigs The bbmap step helped me find the insert point of my novel genes in the virus I'm new to assembly, but this pipeline was just what I was looking for. ...
written 3.3 years ago by aindap120
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denovo-assembly with novel genes inserted
... I have a viral strain with non-viral sequences inserted in. I aligned to my reads to a reference strain. The reads that didn't align, I did a denovo assembly with SSAKE to identify my contigs of my non-viral sequences. What I want is a final assembly of my virus strain where I know the non-viral ...
assembly denovo assembly ilumina written 3.3 years ago by aindap120 • updated 3.3 years ago by Brian Bushnell17k
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what do read with blue outline represent in IGV?
... Dumb question, but I can't seem to find the answer in the IGV docs. I am unable to upload a screenshot due to restrictions, but I am viewing my alignments of Illumina PE reads aligned with BWA mem. Do the reads with a blue outline indicate improper insert size? ...
alignment igv written 3.3 years ago by aindap120 • updated 3.3 years ago by Biomonika (Noolean)3.1k
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finding repeats in de-novo assembled contig from PacBio reads
... Dear BioStars Community: I performed a de-novo assembly of PacBio reads using [Canu][1] for a viral genome. I have my resulting unitig from the canu pipeline. I am now interested in characterizing repeats in my resulting assembly. I'm new to assembly and repeat identification. One simple approach ...
assembly repeat pacbio written 3.4 years ago by aindap120 • updated 3.3 years ago by arnstrm1.8k

Latest awards to aindap

Scholar 7 weeks ago, created an answer that has been accepted. For A: Hisat2 error: --read-lengths arg must be at least 20
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Read Simulation With Mason - Snp Positions
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Error correcting PacBio reads prior to alignment with bwa mem
Popular Question 2.3 years ago, created a question with more than 1,000 views. For GeneSCF and P-value Benjamini and Hochberg (FDR)
Popular Question 2.3 years ago, created a question with more than 1,000 views. For what do read with blue outline represent in IGV?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Interleaving Records From More Than One Fasta File
Popular Question 5.7 years ago, created a question with more than 1,000 views. For Read Simulation With Mason - Snp Positions
Popular Question 6.7 years ago, created a question with more than 1,000 views. For Interleaving Records From More Than One Fasta File
Autobiographer 6.7 years ago, has more than 80 characters in the information field of the user's profile.
Student 7.2 years ago, asked a question with at least 3 up-votes. For Interleaving Records From More Than One Fasta File

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