Activity for Bowtie
-
Bowtie released /bowtie2/2.5.4/bowtie2-2.5.4-source.zip
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
Raja Rajeshwari posted a comment on discussion Bowtie Help
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"><meta name="Generator" content="Microsoft Word 15 (filtered medium)"><style><!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0in; font-size:11.0pt; font-family:"Calibri",sans-serif;} a:link, span.MsoHyperlink {mso-style-priority:99; color:blue; text-decoration:underline;}...
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
likanase33 posted a comment on discussion Bowtie Help
I am having hassle building in index file from a fasta record… IAs you could see under calculus tutor, I am getting a warning: "Encountered empty reference series" and an mistakes:
-
-
-
-
-
-
-
-
shan most posted a comment on discussion Bowtie Developers
I'm using this software in my device and blog and it's working perfectly fine.
-
MP posted a comment on ticket #349
Were you able to fix this error? Command: bowtie2-build --wrapper basic-0 $/home/Kaleb.gatto/Bowtie2/bowtie2-2.2.8/example/reference/lambda_virus.fa lambda_virus
-
Let me share the error file, that way you could explain me better. Are you referring genome.txt file to be a reference genome file? I removed all sequences containing Ns from the fasta file. # reads processed: 11120169 # reads with at least one reported alignment: 40701 (0.37%) # reads that failed to align: 11079468 (99.63%) Reported 40701 alignments # reads processed: 11120169 # reads with at least one reported alignment: 0 (0.00%) # reads that failed to align: 11120169 (100.00%) No alignments #...
-
Let me share me error file, that way you could explain me better. Are you referring genome.txt file to be a reference genome file? I removed all sequences conjtaing Ns from the fasta file. # reads processed: 11120169 # reads with at least one reported alignment: 40701 (0.37%) # reads that failed to align: 11079468 (99.63%) Reported 40701 alignments # reads processed: 11120169 # reads with at least one reported alignment: 0 (0.00%) # reads that failed to align: 11120169 (100.00%) No alignments # reads...
-
Rone Charles posted a comment on discussion Bowtie Help
bowtie-build seems to think that your genome.txt file contains long stretches of, or all, Ns and therefore unable to build an index.
-
Hi, did you figured out the above error message? if yes, Could you help me out. Thank you
-
-
-
-
-
-
-
-
-
-
-
Danielle Lema posted a comment on discussion Bowtie Help
I ran bowtie 2 against a reference genome and it worked perfectly. After saving the data to external, I deleted the paired-end reads from my hpc directory. Later, we decided to align reads against the mito-genome, so I uploaded the same exact files to my directory, and running the exact same command on the exact same files (but with different reference), I got the error " Error, fewer reads in file specified with -2 than in file specified with -1" I know the files have the same number of reads because...
-
-
-
-
Rodolfo.Aramayo posted a comment on ticket #358
Please close this ticket The command issued should have been: bowtie2 \ -t \ -p 20 \ -x /path/to/index/GCA_000001405.15_GRCh38_no_alt_analysis_set \ -q \ -U /data/fastq_file.fq \ --very-sensitive \ --un /data/requested_unaligned_fastq_file.fq -S /data/requested_sam_file.sam; This is "--un" and not "-un" Small typo caused a lot of self-induced pain Apologies for the disturbance...and cheers...
-
noname created ticket #359
(ERR): bowtie2-align died with signal 7 (BUS) (core dumped)
-
Apologies, the second command should read: bowtie2 \ -t \ -p 20 \ -x /path/to/index/GCA_000001405.15_GRCh38_no_alt_analysis_set \ -q \ -U /data/fastq_file.fq \ --very-sensitive \ -S /data/requested_sam_file.sam;
-
Unaligned File Request Triggers Bowtie2 to Fail
1 >