User: Adrian Pelin

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Adrian Pelin2.3k
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Comparative and Population Genomics of Microsporidia. Comparative and Functional Genomics of Cryptomycotans.

Posts by Adrian Pelin

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HISAT2/stringtie: intron impact on expression
... Hello, I was wondering if reads that map to introns or reads that are not in CDS features are considered/included in the calculations of TPM and FPKM? If so, is there any way to exclude those? One would only want mature mRNA expression levels no? I should emphasize I am interested in only protei ...
tpm stringtie mrna expression rna-seq hisat2 written 1 hour ago by Adrian Pelin2.3k
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Comment: C: Generating Interaction map
... Haven't considered that, will give it a shot thanks! ...
written 6 weeks ago by Adrian Pelin2.3k
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Generating Interaction map
... I want to bridge 2 protein interaction networks from 2 different papers. The first dataset consists of protein-protein interactions in the human genome in the format: Bait_A - Pray_1 Bait_A - Pray_2 Bait_A - Pray_3 Bait_B - Pray_1 Bait_B - Pray_4 The second dataset consist of ...
R cytoscape interactome written 6 weeks ago by Adrian Pelin2.3k • updated 6 weeks ago by Jean-Karim Heriche20k
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Comment: C: HISAT2 output direct to bam
... Ok, it makes sense to pipe to sort like https://www.biostars.org/u/4407/ and yourself suggested. What is the impact on RAM usage? Piping to unsorted bam can be done on the go. Do you need to load the whole output into memory in order for you to sort? ...
written 11 weeks ago by Adrian Pelin2.3k • updated 11 weeks ago by ATpoint19k
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HISAT2 output direct to bam
... Hello, HISAT2 can only output sam files, which can be quite large. I found an option to output only reads that mapped to the reference but still the files can be 100s of GB. Is there any issue in directly converting to bam as such: ${hisat2}/hisat2 -p 4 --rg-id=${4} -x $l --dta ${strand} --no ...
samtools rna-seq written 11 weeks ago by Adrian Pelin2.3k • updated 11 weeks ago by ATpoint19k
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Comment: C: hisat2 command line fastq to bam
... What happens if you: hisat2 -f -x hg19_indexed -1 reads_R1.fq -2 reads_R2.fq | samtools view -bSh > eg2.bam Just wondering if you could save space by skipping the storage of sam files ...
written 3 months ago by Adrian Pelin2.3k
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Comment: C: Extracting sequence and annotation of a particular gene
... Very elegant, thanks! It seems your script may neglect strand info when it comes to annotation. Since getfasta gets a forward sequence for something that is minus stranded, the annotations likely needed to be reshaped as well. In your case, regardless of strand the coordinates are simply brought to ...
written 3 months ago by Adrian Pelin2.3k
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Comment: C: Virus RNA Seq reads mapping with salmon
... I would use bbsplit to separate the host (sheep?) reads and virus reads. You can map to multiple references. The command below will create files for ecoli reads, salmonella reads as well as reads that don't map to either. bbsplit.sh in1=reads1.fq in2=reads2.fq ref=ecoli.fa,salmonella.fa basenam ...
written 4 months ago by Adrian Pelin2.3k
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Extracting sequence and annotation of a particular gene
... Hello, I have the human and mouse GENCODE annotations and the genome that goes with it. I am interested to create sequence and annotation files for individual genes. For instance, if I am interested in RSAD2, I can easily find all annotations in the GTF file. What I want is to first extract the ent ...
gtf annotation written 4 months ago by Adrian Pelin2.3k • updated 4 months ago by ATpoint19k
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Answer: A: Virus RNA Seq reads mapping with salmon
... Which poxvirus are you sequencing? I do this all the time with Vaccinia, except I use HISAT and StringTie to quantify transcript levels. Which ever poxvirus you have, you can always extract the CDS regions and treat that as the transcriptome, not a lot of splicing happening in poxviruses.... ...
written 4 months ago by Adrian Pelin2.3k

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Teacher 7 months ago, created an answer with at least 3 up-votes. For C: Demultiplexing fastq files. Undocumented Illumina feature.
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