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Michael Dondrup
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yp19
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telroyjatter
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Recent Replies
Answer: How to filter reads only with single SNV
by
Pierre Lindenbaum
135k
filter with edit-distance NM==1
samtools view -e '[NM]==1'
Comment: Is Biopython a Package or Library?
by
Istvan Albert
87k
correct,
in the more "modern" naming schemes we recommend lowercasing modules and title-case classes to better communicate their type, i…
Answer: Looking for a Whole Genome Sequencing GrCH38 Control group of roughly 250 sample
by
4galaxy77
▴
420
As the comments have said the 30x 1000 genomes genotypes aligned to gr38 can be found here:
http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data…
Answer: how to run and use the ENCODE ATAC-seq pipline
by
Jeremy Leipzig
20k
you might want to check out https://truwl.com/ - they have the official ENCODE ATAC-Seq pipeline as a runnable workflow
Comment: Can too high of a ChIPQC RiP% be indicative of insufficient stringency in peak c
by
ATpoint
48k
TFs can well have FRiPs in the 20% or 30% range, it is all on the antibody, expression level of the protein and quality of the chromatin. …
Comment: htseq-count Error '_StepVector_Iterator_obj' object has no attribute 'next'
by
lieven.sterck
11k
I see, should be OK then I assume.
I remember that we needed to use the version that was installed in the python libs of a specific python…
Comment: htseq-count Error '_StepVector_Iterator_obj' object has no attribute 'next'
by
Sara
•
0
I am using Python 3.7 (htseq-count specifies Python >=3.6)
Comment: Split fasta based on symbol and numeric position in header
by
Nick Scales
•
0
If possible in one step that would be great but I have already worked out how to do the second part of that with bedtools, for this I just …
Comment: Split fasta based on symbol and numeric position in header
by
Nick Scales
•
0
Okay this is super helpful thank you. My only need for the database is for it to have a fasta entry for each CAZyme so I can blast metageno…
Comment: htseq-count Error '_StepVector_Iterator_obj' object has no attribute 'next'
by
lieven.sterck
11k
are you using the correct python version?
Comment: Split fasta based on symbol and numeric position in header
by
GenoMax
100k
Just to clarify you want it to keep track of the aa number and then create a new record for each ID separated by `+` by taking into account…
Comment: Split fasta based on symbol and numeric position in header
by
heskett
•
0
You need to explain what functions you want the database to have. if you use GTF format than this will be readable by alignment programs su…
Comment: Looking for a Whole Genome Sequencing GrCH38 Control group of roughly 250 sample
by
heskett
•
0
As mentioned, raw sequencing data of humans is privacy protected by law because it is identifiable. You need to either use a high-level sum…
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