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Recent Replies
Answer: Somatic truth set
by
samuel
▴
180
I think I have found an naswer to my own question.
Should anyone have the same question as of March 2023 the relevant data and information…
Answer: GetBM - GERP conservation score for GRCm39
by
Kyle
•
0
Final solution thanks to Ben's help::
# convert df to Grange.
snp_gr <-makeGRangesFromDataFrame(BM_SNPs, seqnames.field = "seqnam…
Answer: MapSplice2 gives error if the thread count (-p value) is greater than 2
by
vishal.koparde
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10
Any updates??
Comment: how to know what adapter sequences to trim for RNA-seq?
by
lunarskye222
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Do you happen to know if the middle part of this udi barcode (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCTACATATCTCG) is also part of the TruSeq a…
Comment: Hard clip fastq
by
GenoMax
127k
If you simply want the reads to be compatible in length then do not adapter trim.
Comment: Hard clip fastq
by
samuel
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180
@ATpoint, so no adapter trimming first? Just trim the raw fastq?
Answer: Confused on strandedness, what are antisense transcripts?
by
dsull
★
4.0k
RNA pol always transcribes 5' -> 3'. This has nothing to do with +/-.
Think of it on the DNA level: If the mRNA made is the same sequenc…
Comment: Protein name in GenBank
by
GenoMax
127k
If you must do this programmatically then collect all cases where things differ in order of words (or number of words) like the example abo…
Answer: Hard clip fastq
by
GenoMax
127k
You can also use `reformat.sh` from [**BBMap suite**][1] as follows
reformat.sh -Xmx2g in1=R1.fq.gz in2=R2.fq.gz out1=R1_trim.fq.gz …
Answer: Hard clip fastq
by
ATpoint
70k
Use `seqtk trimfq`. It makes sense to trim first to your desired length and then run identical downstream processing for a fair comparison.…
Comment: Protein name in GenBank
by
Mensur Dlakic
★
23k
I think you either take time to do it properly, or you will end up missing some proteins. BLAST sequence search, even on 1500 genomes, can …
Comment: Log2 FC Threshold
by
ATpoint
70k
Since OP is using GEO2R which uses limma the appropriate function (need to run manually, GEO2R does not support) is `limma::treat()` rather…
Answer: Adding median value to VlnPlot in Seurat
by
Ming Tommy Tang
★
2.9k
If you know ggplot2, you can `get_expression_data` function in here https://divingintogeneticsandgenomics.rbind.io/post/how-to-do-gene-corr…
Answer: how to know what adapter sequences to trim for RNA-seq?
by
Ming Tommy Tang
★
2.9k
You may use fastp which detect adaptors by itself https://github.com/OpenGene/fastp#adapters
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