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Answer: JASPAR2024_getMatrixSet error
by
Raghad
•
0
Try this:
#Read the motifs
library(JASPAR2024)
library(TFBSTools)
jaspar <- JASPAR2024()
sq24 <- RSQLite::dbCo…
Answer: How to convert normalized BigWig file to count matrix?
by
ATpoint
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It's not possible. Gene counts are a region aggregate, bigwigs are a per-base readout and you cannot use normalized counts for mentioned to…
Comment: bcftools - reducing to "sites-only"?
by
Pierre Lindenbaum
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> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: bcftools - reducing to "sites-only"?
by
Matthew
•
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Thank you Pierre!
Not sure why I didn't notice that (I should have)
Comment: How to convert normalized BigWig file to count matrix?
by
Pierre Lindenbaum
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bigwig is chrom/start/end/value . what kind of matrix do you want ?
Comment: How to convert normalized BigWig file to count matrix?
by
feather-W
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I want to use the matrix derived from bigwig files to perform different analysis by DESeq2 or edgeR.
Answer: Have you ever obtained user guide of ExomeCNV?
by
michael.s
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I have uploaded the ExomeCNV (v1.4) user manual [here][1].
[1]: https://fastupload.io/hZbU
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I assume you mean "server" as in local hardware that you own/control since "cloud" is a just bunch of servers on internet that you rent (pa…
Answer: Server or aws cloud- which one is better for gatk pipeline
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I think that is more a matter of convenience and legality. It mostly depends on who pays for it and what you prefer. Both solutions should …
Comment: How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when ru
by
Pierre Lindenbaum
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> could you please explain what the collate does?
http://www.htslib.org/doc/samtools-collate.html
Comment: ComBat_Seq stuck adjusting the data
by
Jaïr
•
0
Same keeps happening to me; but it is weird, I corrected the batch effect with the same exact function a few months ago and worked fine. I …
Comment: How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when ru
by
Lila M
★
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Thank you for the feedback! I already used just the `samtools fastq -1 R1.fq.gz -2 R2.fq.gz -s Rx.fq.gz -0 R0.fq.gz`. Could you please exp…
Comment: Nextflow: how to get the process work dir, within the process
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Answer: How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when ru
by
Pierre Lindenbaum
161k
faster use samtools collate+ fastq
samtools collate -uOn128 in.bam TMPDIR | samtools fastq -1 R1.fq.gz -2 R2.fq.gz -s Rx.fq.gz -0 R…
Comment: Nextflow: how to get the process work dir, within the process
by
ScottDansk
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legend thank you so much!
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