User: Tom_L

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Tom_L260
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Posts by Tom_L

<prev • 32 results • page 1 of 4 • next >
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Comment: C: How to align mouse transcriptome data using bowtie2?
... You can either concatenate all chromosomes into a single file or download a single file that directly contains all chromosomes. Usually, software work with a single file as it is simpler to handle. See here for mm10 genome version: http://hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips/ ...
written 4 months ago by Tom_L260
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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 8 months ago by Tom_L260
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Answer: 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 8 months ago by Tom_L260
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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 8 months ago by Tom_L260
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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 9 months ago by Tom_L260
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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 9 months ago by Tom_L260
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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 11 months ago by Tom_L260
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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 11 months ago by Tom_L260
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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 11 months ago by Tom_L260
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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 12 months ago by Tom_L260

Latest awards to Tom_L

Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: How can I integrate gene with PPI network
Appreciated 11 months ago, created a post with more than 5 votes. For A: How can I integrate gene with PPI network
Scholar 12 months ago, created an answer that has been accepted. For A: Getting sample information from GEO
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How can I integrate gene with PPI network
Teacher 18 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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