User: mgmohsen

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Posts by mgmohsen

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Comment: C: STAR --quantMode GeneCounts always gives 0 counts
... Yes they match. And also, I just tried aligning some other fastq sets and those seem to work normally. It seems like there might be something wrong with this set of fastqs in particular. ...
written 5 weeks ago by mgmohsen0
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Comment: C: STAR --quantMode GeneCounts always gives 0 counts
... Hm, but I've given it in a gtf in the genome indexing step. Does it also need to be specified during alignment? ...
written 5 weeks ago by mgmohsen0
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STAR --quantMode GeneCounts always gives 0 counts
... I'm trying to perform an alignment using `STAR` and extract gene count information. Here is the command I entered: STAR --runThreadN 16 --readFilesCommand zcat --quantMode GeneCounts --genomeDir /path/to/genome/dir --readFilesIn /path/to/file_R1.fastq.gz /path/to/file_R2.fastq.gz However, when ...
alignment written 5 weeks ago by mgmohsen0 • updated 5 weeks ago by swbarnes26.2k
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Comment: C: STAR alignment - segmentation fault error
... Yes! This was the issue, both R1/R2 files need to be supplied at once. Thank you for all your help. ...
written 6 weeks ago by mgmohsen0
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Comment: C: STAR alignment - segmentation fault error
... Yes, I saved it somewhere else, and it has a very similar ending to yours. I'm using a pre-compiled version of `STAR` (version 2.7.1a). Jul 03 12:10:33 ... writing SAindex to disk Writing 8 bytes into ./star_index/SAindex ; empty space on disk = 172171319050240 bytes ... done Writing 12 ...
written 6 weeks ago by mgmohsen0
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Comment: C: STAR alignment - segmentation fault error
... Command used to generate `STAR` index: STAR --runThreadN 16 --runMode genomeGenerate --genomeDir ./star_index --genomeFastaFiles ./GRCh38.p12.genome.fa --sjdbGTFfile ./gencode.v30.annotation.gtf Output of `du -shc *` 26K chrLength.txt 50K chrNameLength.txt 26K chrName ...
written 6 weeks ago by mgmohsen0
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Comment: C: STAR alignment - segmentation fault error
... Yes, I generated the indexes with the same version of `STAR` and there was no error during the process. However, this alignment is my first attempt to test them, so they are not known to work. Is there any standard test that I can do to make sure there's no problem with my indexes? ...
written 6 weeks ago by mgmohsen0
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Comment: C: STAR alignment - segmentation fault error
... Thanks for the recommendation, I will be sure to increase RAM to 40G for future job submissions.. However, I'm still getting the same error for this alignment, even after setting it to 40G of RAM. ...
written 6 weeks ago by mgmohsen0
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Comment: C: STAR alignment - segmentation fault error
... OK, that was definitely the issue with the subset of 1000 that I generated. Trying again, I got the same error as I did with the original fastq read. This seems to indicate that the issue isn't with memory usage. ...
written 6 weeks ago by mgmohsen0
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Comment: C: STAR alignment - segmentation fault error
... Here are the first 10 lines: @COOPER:276:H2HTMBBXY:7:1101:10003:1209 1:N:0:NTTGTACT NTGATGAGTGAGTGTCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTACTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAACAA + #AAFFJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ& ...
written 6 weeks ago by mgmohsen0

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