User: carolgalah

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carolgalah0
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Posts by carolgalah

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Comment: C: FPKM and DESEq - RNAseq
... Thanks for your reply! The STAR returns me the following files: BAM and reads by genes .... I get the featurecounts of the BAM files, correct? After generating the featurecounts, I run DESEq, as well as PCA. ...
written 9 weeks ago by carolgalah0
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FPKM and DESEq - RNAseq
... Hi.. I'm new to RNAseq and bioinformatics... I aligned my samples with STAR, after aligning.... I got the value of FPKM through the cufflinks. I have 2 groups (treated and untreated) each group has 4 samples. I have FPKM value for each sample... Can I get the genes differentially expressed betwe ...
fpkm deseq2 rna-seq written 9 weeks ago by carolgalah0 • updated 9 weeks ago by dz235350
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Comment: C: Genome Index and Alignment- STAR
... Thanks for your reply... I have two bam: rw-rw-r-- 1 acamar2 acamar2 22G Dez 3 16:12 fastqAligned.sortedByCoord.out.bam -rw-rw-r-- 1 acamar2 acamar2 25G Dez 3 15:37 fastqAligned.toTranscriptome.out.bam I need use just this fastqAligned.sortedByCoord.out.bam... correct? Thank you for the advic ...
written 10 weeks ago by carolgalah0
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Comment: C: Genome Index and Alignment- STAR
... Hi, After alignment, I need to run the Cufflinks for assembly and quantify transcripts. I need to indicate only my file Aligned.sortedByCoord.out.bam, or do I need to indicate my raw data + Aligned.sortedByCoord.out.bam.? Do I need to index the Aligned.sortedByCoord.out.bam? thanks ...
written 10 weeks ago by carolgalah0
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Comment: C: Genome Index and Alignment- STAR
... My files after the alignment: -rw-rw-r-- 1 acamar2 acamar2 22G Dez 3 16:12 fastqAligned.sortedByCoord.out.bam -rw-rw-r-- 1 acamar2 acamar2 25G Dez 3 15:37 fastqAligned.toTranscriptome.out.bam -rw-rw-r-- 1 acamar2 acamar2 1,9K Dez 3 16:12 fastqLog.final.out -rw-rw-r-- 1 acamar2 ...
written 10 weeks ago by carolgalah0 • updated 10 weeks ago by Devon Ryan88k
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Comment: C: Genome Index and Alignment- STAR
... Sorry for the delay in replying ... Now it worked, I had not tried the use of gunzip -c, I had forgotten all the time to use the (-c), beginner error. Sorry for the inconvenience! Another question: Star generates a directory named BAMsort, with several other folders. In those directories should ha ...
written 10 weeks ago by carolgalah0
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Comment: C: Genome Index and Alignment- STAR
... Sorry for the delay in replying ... Now it worked, I had not tried the use of gunzip -c, I had forgotten all the time to use the (-c), beginner error. Sorry for the inconvenience! Another question: Star generates a directory named BAMsort, with several other folders. In those directories should ha ...
written 10 weeks ago by carolgalah0
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Comment: C: Genome Index and Alignment- STAR
... I tried everything again ... and nothing worked. I recreated the genome index with toplevel. I ran the STAR using only 1 pair of samples. I tried aligning it with a couple of samples using the toplevel genome, also tried using the genome with all the chr files ... but nothing worked. What will happe ...
written 11 weeks ago by carolgalah0
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Comment: C: Genome Index and Alignment- STAR
... I tried everything again ... and nothing worked. I recreated the genome index with toplevel. I ran the STAR using only 1 pair of samples. I tried aligning it with a couple of samples using the toplevel genome, also tried using the genome with all the chr files ... but nothing worked. What will happe ...
written 11 weeks ago by carolgalah0
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Comment: C: Genome Index and Alignment- STAR
... `--genomeDir /home/acamar2/files/Rnor_6.0` Rnor_6.0 is directory where the files of the genome: drwxr-xr-x 2 acamar2 acamar2 4.0K Nov 28 15:58. drwxr-xr-x 5 acamar2 acamar2 50 Nov 28 15:58 .. -rw-rw-r-- 1 acamar2 acamar2 217 Nov 28 14:56 chrLength.txt -rw-rw-r-- 1 acamar2 acamar2 2 ...
written 11 weeks ago by carolgalah0 • updated 11 weeks ago by Devon Ryan88k

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