User: Joel Wallenius

Reputation:
10
Status:
New User
Location:
Sweden
Last seen:
5 hours ago
Joined:
1 year, 6 months ago
Email:
j************@gmail.com

MSc in Bioinformatics at Lund University.

Primarily interested in solving the aging problem. Eternal youth for everybody woop woop!

Background in astrophysics. I would rather program than think about study designs.

Posts by Joel Wallenius

<prev • 39 results • page 1 of 4 • next >
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Comment: C: Calculating FPKM and TPM by hand from htseq-count output?
... Many things one should do, yes. PI wants FPKM, I oblige. Thanks anyway! ...
written 8 days ago by Joel Wallenius10
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Comment: C: Calculating FPKM and TPM by hand from htseq-count output?
... OK thanks!! I've wondered about the FPKM's myself since TPM's seem better (but not even TPM's are wholly 'liked' by the community it seems), but the others in my research group said FPKM is the standard measure in our field (leukemia), so I just rolled with it. Somehow the libraries are supposed to ...
written 9 days ago by Joel Wallenius10
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Comment: C: Calculating FPKM and TPM by hand from htseq-count output?
... Do you mean 'mapped' as in mapped to the genome, or mapped to an exon in my gtf file? The difference between these two numbers is quite large. Several million reads! ...
written 9 days ago by Joel Wallenius10
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Calculating FPKM and TPM by hand from htseq-count output?
... Hello! I am counting reads with htseq-count, and wasted some hours trying to find an extant software that would calculate FPKM and/or TPM from that output, so I wrote a script myself. There is just one question mark - should the denominator (the sum of reads within the sample) be the sum of the re ...
htseq fpkm tpm rna-seq written 9 days ago by Joel Wallenius10
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Answer: A: Approximately following the GATK recommended workflow for DNA sequence data, my
... SOLVED! ( Sorry I couldn't write this earlier, my post limit had been reached ) The problem was that my targets file (BED-format) used chromosome names 1,2,3,4,5,6..., while my alignment files used names like chr1,ch2,chr3... Big thanks to everyone for you patience. I'll remember your advice! ...
written 27 days ago by Joel Wallenius10
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Comment: C: Approximately following the GATK recommended workflow for DNA sequence data, my
... Your question gave me an idea. I am using a file with targets in a BED-format, and the chromosome names in that file were like 1,2,3... rather than chr1, chr2, and so on... that's why the output was empty. :[ The shame is real. At least the problem is solved now... ...
written 28 days ago by Joel Wallenius10
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Comment: C: Approximately following the GATK recommended workflow for DNA sequence data, my
... I'm not sure actually, I only know that the input at the start of my script is in .fastq.gz format, that the reads are paired, and produced by an Illumina machine. FWIW, all the reads and all the samples have the same adapter sequences. Does that supply enough information? ...
written 28 days ago by Joel Wallenius10
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Comment: C: Approximately following the GATK recommended workflow for DNA sequence data, my
... Added all the commands in order! ...
written 28 days ago by Joel Wallenius10
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Comment: C: Approximately following the GATK recommended workflow for DNA sequence data, my
... Yes true but this script is supposed to be used by the rest of my research group and they aren't very savvy, if you know what I mean. I'd like to make it as easy as possible for them, and installing a bunch of packages as a first step is... well, it's not a priority right now at least. Perhaps in a ...
written 28 days ago by Joel Wallenius10
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Comment: C: Approximately following the GATK recommended workflow for DNA sequence data, my
... They use a module system, you load modules more or less like you'd activate virtual envs. The latest GATK module is 3.7 or something. I could maybe ask the admins to install the latest one but that would take a while, probably. How much do I stand to gain in practice from an update? The problem I'm ...
written 28 days ago by Joel Wallenius10

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Popular Question 11 months ago, created a question with more than 1,000 views. For The meaning of '0' allele frequency in vcftools output
Autobiographer 19 months ago, has more than 80 characters in the information field of the user's profile.

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