Error while mapping raw reads to genome using tophat2

Question

[Bioinfonext]

Deal All,

I getting error while mapping raw reads to genome using tophat2: Please suggest how to solve it.

[2017-01-15 05:09:52] Resuming TopHat pipeline with unmapped reads

[2017-01-15 05:09:52] Mapping left_kept_reads.m2g_um to genome genome_index with Bowtie2

[2017-01-15 06:32:14] Mapping left_kept_reads.m2g_um_seg1 to genome genome_index with Bowtie2 (1/5)

[2017-01-15 06:45:17] Mapping left_kept_reads.m2g_um_seg2 to genome genome_index with Bowtie2 (2/5)

[2017-01-15 06:59:09] Mapping left_kept_reads.m2g_um_seg3 to genome genome_index with Bowtie2 (3/5)

[2017-01-15 07:13:04] Mapping left_kept_reads.m2g_um_seg4 to genome genome_index with Bowtie2 (4/5)

[2017-01-15 07:26:16] Mapping left_kept_reads.m2g_um_seg5 to genome genome_index with Bowtie2 (5/5)

[2017-01-15 07:35:22] Mapping right_kept_reads.m2g_um to genome genome_index with Bowtie2

[2017-01-15 09:04:09] Mapping right_kept_reads.m2g_um_seg1 to genome genome_index with Bowtie2 (1/5)

[2017-01-15 09:20:25] Mapping right_kept_reads.m2g_um_seg2 to genome genome_index with Bowtie2 (2/5)

[2017-01-15 09:35:23] Mapping right_kept_reads.m2g_um_seg3 to genome genome_index with Bowtie2 (3/5)

[2017-01-15 09:50:10] Mapping right_kept_reads.m2g_um_seg4 to genome genome_index with Bowtie2 (4/5)

[2017-01-15 10:05:27] Mapping right_kept_reads.m2g_um_seg5 to genome genome_index with Bowtie2 (5/5)

[2017-01-15 10:17:04] Searching for junctions via segment mapping

[FAILED]

Error: segment-based junction search failed with err =127

/home/yog/software/tophat-2.1.1/src/segment_juncs: error while loading shared libraries: libboost_thread.so.1.62.0:

cannot open shared object file: No such file or directory

[Brian Bushnell]

It appears that you don't have boost installed. But, I think it's probably faster and easier to install and run BBMap instead of TopHat.

[WouterDeCoster]

Tophat is deprecated and instead you should use it's successor HISAT2 or alternative aligners such as STAR or BBMap.

[Bioinfonext]

Please share the link for HISAT2 and cammand line to install it on cento OS linux platform.

[WouterDeCoster]

Please do some work/searching on your own. The manual is quite clear.

[Bioinfonext]

Thanks, I am able to install it.

[WouterDeCoster]

See, wasn't so hard.

[GenoMax]

Where/how did you download/install TopHat?

[Bioinfonext]

Now I am not sure from where I downloaded tophat2. Can you suggest how to uninstall it and is it possible to install boost library with tophat2?

If yes, please share the link and installation cammand line.

[GenoMax]

There should be no install needed if you download pre-compiled binary for TopHat. But that said you should consider switching to a newer program from ones suggested in this thread.