User: carolgalah

gravatar for carolgalah
carolgalah0
Reputation:
0
Status:
New User
Last seen:
2 days, 12 hours ago
Joined:
2 weeks, 5 days ago
Email:
c*********@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by carolgalah

<prev • 16 results • page 1 of 2 • next >
0
votes
0
answers
161
views
0
answers
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 2 days ago by carolgalah0
0
votes
0
answers
161
views
0
answers
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 2 days ago by carolgalah0
0
votes
0
answers
161
views
0
answers
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 5 days ago by carolgalah0 • updated 4 days ago by Devon Ryan86k
0
votes
0
answers
161
views
0
answers
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 5 days ago by carolgalah0
0
votes
0
answers
161
views
0
answers
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 5 days ago by carolgalah0
0
votes
0
answers
161
views
0
answers
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 9 days ago by carolgalah0
0
votes
0
answers
161
views
0
answers
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 9 days ago by carolgalah0
0
votes
0
answers
161
views
0
answers
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 10 days ago by carolgalah0 • updated 10 days ago by Devon Ryan86k
0
votes
0
answers
161
views
0
answers
Comment: C: Genome Index and Alignment- STAR
... I tried to use exactly this script with the toplevel. Is it some mistake in my samples? Always before generating the genome, I unzipped the FASTA files. I need to unzip this file: -rw-rw-r-- 1 acamar2 acamar2 2,7G Nov 28 15:49 Genome ...
written 10 days ago by carolgalah0
0
votes
0
answers
161
views
0
answers
Comment: C: Genome Index and Alignment- STAR
... I tried to use the toplevel, but it also didn't work. They gave the same results. When I run the alignment, do I need to put the FASTA and GTF file in the same folder as the genome? ...
written 10 days ago by carolgalah0

Latest awards to carolgalah

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1413 users visited in the last hour