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Recent Replies
Answer: demultiplexing with guppy_basecaller and guppy_barcoder using --detect_mid_stran
by
Yuri
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0
Hi @and did you ever figure out why guppy was resulting in 90% of reads in unclassified folder?
I am running into the same issue, and am…
Comment: Retrieve hgnc_symbol from XM_ refseqs using BiomaRt
by
ladina.hoesli
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Thank you very much, this helps a lot!
Answer: Snakemake vs Nextflow Upcoming bioinformatics Project
by
cfos4698
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720
There are a lot of votes for Nextflow here, and it's generally pretty popular (and increasing in popularity). As a 'dissenting' voice, I'll…
Answer: Is it possible to use pseudoalignments.bam to run rMATs?
by
dsull
★
4.0k
No, you can't do that with kallisto's bam files. For one, kallisto (by default) doesn't map to introns which is required by rMATs.
You c…
Answer: genome annotation [sstart] [send] - how to get protein sequence from gene
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shenwei356
8.0k
It means that the gene is on the negative/minus strand. So you need to compute the reverse complementary sequence before translating it to …
Answer: When to merge multiple fastq files into one for RNAseq analysis?
by
GenoMax
127k
As long as the sample name matches across the lanes they are pieces of the same sample.
> I was thinking of combining the two fastq files…
Comment: Kallisto bustools for scRNA-seq
by
dsull
★
4.0k
Yes, just put that fastq file (it'll be the same as any other kallisto bustools run, except you have just one fastq file and you have that …
Comment: Error building snpEff database "Transcript 'hypothetical_protein' already exist
by
Jane
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0
Hi,
I have the same issue. After running the command, I run the "sh scripts/buildDbNcbi.sh U00096.2" to download again. Then the same issu…
Answer: bash command to process a line
by
GenoMax
127k
With just one line example not sure if this will work
awk -F '[|_]' '{print $2,$4}' your_file
CU459141.1 CAM87240.1
Comment: RNA Sequencing and Vg pan -transcriptome build
by
kcarery
•
0
Thank you! I found this as well and trying to understand it now.
Comment: RNA Sequencing and Vg pan -transcriptome build
by
kcarery
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0
Thank you so much! This is where I am leading back to as well! I don't have much insights into Hisat2. I am going to give it a go this week…
Comment: How can I easily remove overlapping transcripts, keeping only longest transcript
by
Juke34
7.8k
Interesting, why would you merge genes that are on different strands? They should be different genes. It cannot be done without modifying t…
Comment: featureCounts problem in reading Gff
by
Beatrice
•
0
That's the output, so apparently I have the exon. Anyway, after running grep command the featureCounts worked, even though I didn't change …
Comment: bash command to process a line
by
saadleeshehreen
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110
Yes the word start with lcl| and always sperated by _prot_. I am very naive pattern matching and extraction. I was trying to cut the field …
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