User: Tom_L

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Tom_L210
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Posts by Tom_L

<prev • 31 results • page 1 of 4 • next >
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Comment: C: Trinity: how to avoid out of memory error in butterfly
... Are you sure that the problem comes from how much RAM is required? I believe you ask too many cores to your server: *unable to create new native thread* (https://plumbr.eu/outofmemoryerror/unable-to-create-new-native-thread). Most Trinity problems can be resolved by lowering CPU requirement (16-32 c ...
written 7 weeks ago by Tom_L210
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Comment: C: Human transcription download
... I recommend you to use the information available in the [Table Browser from UCSC][1]. Pick your genome version (hg19 or hg38), choose your annotations (Ensembl, RefSeq, etc.) and get the GTF output format. RefSeq is a good starting point. If you need a transcriptome fasta file, you can use the gtf_t ...
written 7 weeks ago by Tom_L210
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Comment: C: How to statistically compare two unit vectors?
... How about computing the [Wilcoxon's RST][1] ([Shapiro–Wilk][2] test is significant for nw so it is not normally distributed)? I didn't understand if your data is paired or not. If yes, use the [Wilcoxon's signed-RST][3]. [1]: https://en.wikipedia.org/wiki/Mann%E2%80%93Whitney_U_test [2]: http ...
written 7 weeks ago by Tom_L210
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Comment: C: Removal of PCR dupliactes from trimmed reads
... samtools rmdum does not remove duplicates when paired reads map to different chromosomes. Do these 14% duplicates left map to different chromosomes? ...
written 8 weeks ago by Tom_L210
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Comment: C: Enrichment analysis: Which tool I should trust?
... ENCODE resource seems a good starting point (http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeRegTfbsClustered/; try wgEncodeRegTfbsClusteredV3.bed.gz ). This file contains TFBS in BED format. You can grep MEF2 sites and get nearest genes with an short script. Several MEF2 sites next ...
written 8 weeks ago by Tom_L210
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Answer: A: Bam to fastq conversion is giving error?
... No big deal, you just have to sort your bam by read names before converting data as recommended by bedtools (http://bedtools.readthedocs.io/en/latest/content/tools/bamtofastq.html). > BAM should be sorted by query name (samtools sort -n aln.bam aln.qsort) if creating paired FASTQ with this opti ...
written 4 months ago by Tom_L210
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Answer: A: determining cutoff for Kaplan Meier
... Considering gene expression, you should primarily rely on unsupervised approaches such as mean or median split (commonly used). However, I would not recommend the median split since you arbitrary split your cohort in half and I guess that not exactly 50% of patients will survive in your analysis. I ...
written 4 months ago by Tom_L210
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GSEA signal strength
... Hello, I have trouble understanding one of the most important GSEA metrics: the signal strength. According to the documentation (http://software.broadinstitute.org/gsea/doc/GSEAUserGuideTEXT.htm#_HTML_Report): > The enrichment signal strength that combines the two previous statistics: (Tag %) × ...
gsea written 4 months ago by Tom_L210
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Comment: C: Getting sample information from GEO
... No problem. GEOquery actually does the job but requires downloading the SOFT files first. It does not directly query GEO. Moreover: it downloads a 100Mb file per sample if you process them individually. 873 samples times 100Mb each is 87Gb, much more than the 36Gb file available from GEO (whole data ...
written 5 months ago by Tom_L210
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Answer: A: Getting sample information from GEO
... I answer my own question since I found a convenient way to do that. There are two problems with the GEOquery package from BioConductor. First: GEOquery required downloading the whole data again (unless I missed an option to only get sample information?) and the raw dataset is nearly 100 Gb. Knowing ...
written 5 months ago by Tom_L210

Latest awards to Tom_L

Appreciated 4 months ago, created a post with more than 5 votes. For A: How can I integrate gene with PPI network
Scholar 5 months ago, created an answer that has been accepted. For A: Getting sample information from GEO
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How can I integrate gene with PPI network
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How can I integrate gene with PPI network

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