User: prabin.dm

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prabin.dm30
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Posts by prabin.dm

<prev • 20 results • page 1 of 2 • next >
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RSEM with STAR aligment
... I have single-end fastq.gz files. when I run RSEM with `--gzipped-read-file` it says invalid number of cammands and when i dont use it, it says `FATAL ERROR, exiting. What should I do? rsem-calculate-expression --star -star-path /share/pkg/star/2.5.3a -p 4 EH_25_data/EH025x045_L001/L001_R1_00 ...
star rsem written 4 days ago by prabin.dm30
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Do STAR genome index and RSEM reference need to be from same files?
... Hi, I am using STAR for read alignment. The STAR genome index was built on .gtf and .fa downloaded from UCSC genome browser. Should I run rsem-prepare-reference on the same .gtf and .fa files ? Or I can have rsem reference built on gft and fasta files downloaed from different source ? ...
rna-seq rsem star written 7 days ago by prabin.dm30 • updated 7 days ago by WouterDeCoster35k
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Comment: C: STAR alignment error: quantmod not found
... correcting that resulted in the same output. Should I have the `rsem-prepare-reference` run before I use `--quantMode TranscriptomeSAM` ? ...
written 8 days ago by prabin.dm30
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STAR alignment error: quantmod not found
... Hi all, I am using STAR for aligment and gettting an error. I can't figure out why? star 2.5.3a is located under /share/pkg/star/2.5.3a /home/.lsbatch/1544131842.9569914.shell: line 22: --quantMode: command not found Here is my code module load star/2.5.3a STAR -- genomeDir ...
rnaseq alignment star written 8 days ago by prabin.dm30 • updated 8 days ago by Devon Ryan86k
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DGE Analysis between 3 conditions
... Hi, I have datasets for 3 different conditions`["WT", "KO", "KO1"]` (each with 3 replicates). [and two time points[`"0" and "12"`]]. To use in DESeq, I have constructed a DSElist, with design `~ group` where group has 6 levels. dds <- DESeqDataSetFromMatrix(countData = readCount, ...
deseq rna-seq edger written 9 days ago by prabin.dm30
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Comment: C: STAR alignment error: ERROR in input reads
... thank you. I will make that change. Also, I changed the title. ...
written 9 days ago by prabin.dm30
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Comment: C: FASTQ file format
... Thanks again. I will do that. ...
written 9 days ago by prabin.dm30
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Comment: C: FASTQ file format
... Thats looks like an useful utility. When I downloaded it saves as a text file, which I cant run. Can you please let me know how to use it? ...
written 9 days ago by prabin.dm30
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Comment: C: FASTQ file format
... That worked. Thank you While we are at it, can i ask another question? I prepared STAR genome indices with `--sjdbOverhang 99`. Currently the readlength of my fastq files are 75bp. Should I prepare genome indices again ? ...
written 9 days ago by prabin.dm30
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Comment: C: FASTQ file format
... the output for `file L001_R1_001.fastq.gz ` is `L001_R1_001.fastq.gz: gzip compressed data, extra field` and the output for `gunzip -c L001_R1_001.fastq.gz | paste - - - - | cut -c 1 | uniq | sort | uniq ` is `@` ...
written 9 days ago by prabin.dm30

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