User: spaladug

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spaladug10
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United States
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1 month ago
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5 years, 4 months ago
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Posts by spaladug

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Best-suited unit of expression to perform between-sample comparison
... You should use TPM values for within sample comparison. ...
written 7 weeks ago by spaladug10
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Aligning to ultra-short reference sequence
... I have set of subject sequences (25 to 40 bps long). My query sequences are 200-300 bp long. I am trying to find the location of short subject sequences in long query sequences. This is the exact inverse of the alignment problem, where we have long reference and we have short reads that we align to ...
alignment written 2.8 years ago by spaladug10 • updated 2.8 years ago by d-cameron2.3k
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Comment: C: Update third line in fastq file using Biopython
... sorry, fixed the code. it should be record.format, It looks like most of the aligners ignore the third line and I haven't faced any problems with this format in our pipeline. You are right I cannot use SeqIO anymore on this record. But I don't intend to use Biopython after this step is done. ...
written 4.2 years ago by spaladug10
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Answer: A: Update third line in fastq file using Biopython
... Here is my python based solution to this, if anyone else is looking to modify the line with "+" sign: with open(fh, 'w') as unique_file: for record in SeqIO.parse(readsFile, "fastq"): rec = record.format("fastq").splitlines() #compute your stats for this rec ...
written 4.2 years ago by spaladug10
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Comment: C: Update third line in fastq file using Biopython
... Not an incompatible version of fastq, I will be adding info next to + sign, so all the other aligner tools will still work as most of the tools ignore info in the third line. We have tools in our own custom pipeline that read info next to the + sign to compute stats. ...
written 4.2 years ago by spaladug10
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Comment: C: Update third line in fastq file using Biopython
... I need to store information pertaining to each read in the third line. We have other tools in the pipeline that read the third line in each sequence read to compute some stats. ...
written 4.2 years ago by spaladug10
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Update third line in fastq file using Biopython
... Is there a way to update the third line in a fastq file (i.e, lines starting with +) programmatically using Biopython? I can parse the file using SeqIO but I don't know which field to update. Thanks ...
fastq written 4.2 years ago by spaladug10 • updated 4.2 years ago by Alex Reynolds31k
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Answer: A: Conversion of VCF file to Vranges
... The following code should do it: vcf <- readVcf(x, genome = genome) vr <- as(vcf, "VRanges") ...
written 4.9 years ago by spaladug10
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RnaSeq StringTie runtime error
... I am trying to use StringTie for transcript assembly and I am getting a strange error. I was able to run StringTie successfully for two of my samples and I am getting the following error when I run it on my third sample: "Error at GBitVec: index 7 out of bounds (size 7)" Has anybody seen this erro ...
rna-seq written 5.4 years ago by spaladug10 • updated 5.3 years ago by Biostar ♦♦ 20

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Popular Question 2.7 years ago, created a question with more than 1,000 views. For RnaSeq StringTie runtime error
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